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GeneBe

6-26374343-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_007047.5(BTN3A2):c.981G>A(p.Ser327=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 1,611,670 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 36 hom., cov: 29)
Exomes 𝑓: 0.0023 ( 41 hom. )

Consequence

BTN3A2
NM_007047.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.04
Variant links:
Genes affected
BTN3A2 (HGNC:1139): (butyrophilin subfamily 3 member A2) This gene encodes a member of the immunoglobulin superfamily, which resides in the juxta-telomeric region of the major histocompatability class 1 locus and is clustered with the other family members on chromosome 6. The encoded protein may be involved in the adaptive immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-26374343-G-A is Benign according to our data. Variant chr6-26374343-G-A is described in ClinVar as [Benign]. Clinvar id is 768070.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.04 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0133 (2007/150770) while in subpopulation AFR AF= 0.0425 (1744/41046). AF 95% confidence interval is 0.0408. There are 36 homozygotes in gnomad4. There are 941 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 36 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BTN3A2NM_007047.5 linkuse as main transcriptc.981G>A p.Ser327= synonymous_variant 9/11 ENST00000377708.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BTN3A2ENST00000377708.7 linkuse as main transcriptc.981G>A p.Ser327= synonymous_variant 9/111 NM_007047.5 P2P78410-1
ENST00000707189.1 linkuse as main transcriptn.1000-178844G>A intron_variant, non_coding_transcript_variant
ENST00000707191.1 linkuse as main transcriptn.1001-158362G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0133
AC:
2003
AN:
150684
Hom.:
36
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0425
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00822
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000421
Gnomad FIN
AF:
0.0000977
Gnomad MID
AF:
0.0195
Gnomad NFE
AF:
0.00149
Gnomad OTH
AF:
0.00967
GnomAD3 exomes
AF:
0.00455
AC:
1143
AN:
251460
Hom.:
19
AF XY:
0.00350
AC XY:
476
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.0434
Gnomad AMR exome
AF:
0.00717
Gnomad ASJ exome
AF:
0.000695
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.000261
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.00124
Gnomad OTH exome
AF:
0.00489
GnomAD4 exome
AF:
0.00227
AC:
3313
AN:
1460900
Hom.:
41
Cov.:
32
AF XY:
0.00207
AC XY:
1501
AN XY:
726718
show subpopulations
Gnomad4 AFR exome
AF:
0.0419
Gnomad4 AMR exome
AF:
0.00761
Gnomad4 ASJ exome
AF:
0.000536
Gnomad4 EAS exome
AF:
0.000177
Gnomad4 SAS exome
AF:
0.000290
Gnomad4 FIN exome
AF:
0.000131
Gnomad4 NFE exome
AF:
0.00112
Gnomad4 OTH exome
AF:
0.00426
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0133
AC:
2007
AN:
150770
Hom.:
36
Cov.:
29
AF XY:
0.0128
AC XY:
941
AN XY:
73530
show subpopulations
Gnomad4 AFR
AF:
0.0425
Gnomad4 AMR
AF:
0.00822
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000633
Gnomad4 FIN
AF:
0.0000977
Gnomad4 NFE
AF:
0.00149
Gnomad4 OTH
AF:
0.00959
Alfa
AF:
0.00703
Hom.:
5
Bravo
AF:
0.0158
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.00109
EpiControl
AF:
0.00178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
2.5
Dann
Benign
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs115820857; hg19: chr6-26374571; COSMIC: COSV100709527; COSMIC: COSV100709527; API