Variant chr6-26368710-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_007047.5(BTN3A2):c.231C>T(p.Asn77=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 150,964 control chromosomes in the GnomAD database, including 292 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 292 hom., cov: 33)

Exomes 𝑓: 0.24 ( 436 hom. )

Failed GnomAD Quality Control

Consequence

BTN3A2
NM_007047.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.88

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]

BTN3A2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 6-26368710-C-T is Benign according to our data. Variant chr6-26368710-C-T is described in ClinVar as [Benign]. Clinvar id is 770547.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.88 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN3A2	NM_007047.5 linkuse as main transcript	c.231C>T	p.Asn77=	synonymous_variant	4/11	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7 linkuse as main transcript	c.231C>T	p.Asn77=	synonymous_variant	4/11	1	NM_007047.5	ENSP00000366937	P2	P78410-1
	ENST00000707189.1 linkuse as main transcript	n.1000-184477C>T		intron_variant, non_coding_transcript_variant
	ENST00000707191.1 linkuse as main transcript	n.1001-163995C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

35826

AN:

150850

Hom.:

294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.210

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.224

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.238

AC:

345837

AN:

1453892

Hom.:

436

Cov.:

AF XY:

0.238

AC XY:

172050

AN XY:

723452

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.215

Gnomad4 ASJ exome

AF:

0.212

Gnomad4 EAS exome

AF:

0.101

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.237

AC:

35845

AN:

150964

Hom.:

292

Cov.:

AF XY:

0.234

AC XY:

17249

AN XY:

73740

show subpopulations

Gnomad4 AFR

AF:

0.272

Gnomad4 AMR

AF:

0.203

Gnomad4 ASJ

AF:

0.211

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.191

Gnomad4 NFE

AF:

0.241

Gnomad4 OTH

AF:

0.223

Alfa

AF:

0.235

Hom.:

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 05, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.7

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over