6-26368710-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.88

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]

(HGNC:):

ACMG classification

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	UniProt
BTN3A2	NM_007047.5	c.231C>T	p.Asn77=	synonymous_variant	4/11	ENST00000377708.7

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35826 AN: 150850 Hom.: 294 Cov.: 33

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.: 37 AF XY: 0.238 AC XY: 172050 AN XY: 723452

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.: 33 AF XY: 0.234 AC XY: 17249 AN XY: 73740

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.: 49

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

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

Other links and lift over

dbSNP: rs28717012; hg19: chr6-26368938; COSMIC: COSV62686740; COSMIC: COSV62686740;