chr6-26384865-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006995.5(BTN2A2):​c.95-150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 853,386 control chromosomes in the GnomAD database, including 5,252 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.079 ( 592 hom., cov: 32)
Exomes 𝑓: 0.11 ( 4660 hom. )

Consequence

BTN2A2
NM_006995.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157
Variant links:
Genes affected
BTN2A2 (HGNC:1137): (butyrophilin subfamily 2 member A2) Butyrophilin is the major protein associated with fat droplets in the milk. This gene is a member of the BTN2 subfamily of genes, which encode proteins belonging to the butyrophilin protein family. The gene is located in a cluster on chromosome 6, consisting of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The encoded protein is a type I receptor glycoprotein involved in lipid, fatty-acid and sterol metabolism. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BTN2A2NM_006995.5 linkuse as main transcriptc.95-150C>G intron_variant ENST00000356709.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BTN2A2ENST00000356709.9 linkuse as main transcriptc.95-150C>G intron_variant 1 NM_006995.5 P1Q8WVV5-1
ENST00000707189.1 linkuse as main transcriptn.1000-168322C>G intron_variant, non_coding_transcript_variant
ENST00000707191.1 linkuse as main transcriptn.1001-147840C>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0788
AC:
11984
AN:
152166
Hom.:
594
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0339
Gnomad AMI
AF:
0.198
Gnomad AMR
AF:
0.0393
Gnomad ASJ
AF:
0.0415
Gnomad EAS
AF:
0.102
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.0789
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.112
Gnomad OTH
AF:
0.0661
GnomAD4 exome
AF:
0.107
AC:
75157
AN:
701102
Hom.:
4660
AF XY:
0.106
AC XY:
37900
AN XY:
356050
show subpopulations
Gnomad4 AFR exome
AF:
0.0343
Gnomad4 AMR exome
AF:
0.0362
Gnomad4 ASJ exome
AF:
0.0452
Gnomad4 EAS exome
AF:
0.134
Gnomad4 SAS exome
AF:
0.0917
Gnomad4 FIN exome
AF:
0.0831
Gnomad4 NFE exome
AF:
0.117
Gnomad4 OTH exome
AF:
0.0926
GnomAD4 genome
AF:
0.0786
AC:
11975
AN:
152284
Hom.:
592
Cov.:
32
AF XY:
0.0759
AC XY:
5652
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.0339
Gnomad4 AMR
AF:
0.0391
Gnomad4 ASJ
AF:
0.0415
Gnomad4 EAS
AF:
0.103
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.0789
Gnomad4 NFE
AF:
0.112
Gnomad4 OTH
AF:
0.0664
Alfa
AF:
0.0988
Hom.:
99
Bravo
AF:
0.0732
Asia WGS
AF:
0.103
AC:
359
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
8.0
DANN
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs2072806; hg19: chr6-26385093; API