rs3811256

Variant names:

• chr14-22343205-G-A
• rs3811256

Your query was ambiguous. Multiple possible variants found:

• chr14-22343205-G-A
• chr14-22343205-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.296 in 150,732 control chromosomes in the GnomAD database, including 6,953 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 0.30 (6953 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 5 publications found

Genes affected

TRA (HGNC:12027):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22343205G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+57839C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44605 AN: 150614 Hom.: 6947 Cov.: 26

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.281

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 44640 AN: 150732 Hom.: 6953 Cov.: 26 AF XY: 0.302 AC XY: 22212 AN XY: 73602

African (AFR) AF: 0.256 AC: 10494 AN: 40944

American (AMR) AF: 0.275 AC: 4135 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1075 AN: 3458

East Asian (EAS) AF: 0.557 AC: 2855 AN: 5126

South Asian (SAS) AF: 0.482 AC: 2287 AN: 4740

European-Finnish (FIN) AF: 0.334 AC: 3477 AN: 10406

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19387 AN: 67752

Other (OTH) AF: 0.284 AC: 593 AN: 2086

Alfa AF: 0.292 Hom.: 28454

Bravo AF: 0.285

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.84
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs3811256; hg19: chr14-22811629;