rs6802503

Positions:

• chr3-185924102-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004593.3(TRA2B):​c.334-118T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 803,310 control chromosomes in the GnomAD database, including 13,078 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 0.13 (1676 hom., cov: 32)
  • Exomes 𝑓: 0.18 (11402 hom.)
• Consequence: TRA2B NM_004593.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

Genes affected

TRA2B (HGNC:10781): (transformer 2 beta homolog) This gene encodes a nuclear protein which functions as sequence-specific serine/arginine splicing factor which plays a role in mRNA processing, splicing patterns, and gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRA2B	NM_004593.3	c.334-118T>G		intron_variant		ENST00000453386.7
TRA2B	NM_001243879.2	c.34-118T>G		intron_variant
TRA2B	XM_047448717.1	c.34-118T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRA2B	ENST00000453386.7	c.334-118T>G		intron_variant		1	NM_004593.3	P2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19349 AN: 152160 Hom.: 1675 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.135

GnomAD4 exome AF: 0.179 AC: 116345 AN: 651032 Hom.: 11402 Cov.: 9 AF XY: 0.177 AC XY: 58020 AN XY: 328606

Gnomad4 AFR exome AF: 0.0313

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.0955

Gnomad4 EAS exome AF: 0.0600

Gnomad4 SAS exome AF: 0.0661

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.127 AC: 19344 AN: 152278 Hom.: 1676 Cov.: 32 AF XY: 0.121 AC XY: 9042 AN XY: 74456

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.0534

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.134

Alfa AF: 0.173 Hom.: 1652

Bravo AF: 0.126

Asia WGS AF: 0.0450 AC: 156 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs6802503; hg19: chr3-185641890; COSMIC: COSV52025222; COSMIC: COSV52025222;