rs10132760

Variant names:

• chr14-21728267-C-A
• rs10132760

Your query was ambiguous. Multiple possible variants found:

• chr14-21728267-C-A
• chr14-21728267-C-G
• chr14-21728267-C-T

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 0.582 in 152,050 control chromosomes in the GnomAD database, including 27,065 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 0.58 (27065 hom., cov: 32)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 4 publications found

Genes affected

TRA (HGNC:12027):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.21728267C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88451 AN: 151932 Hom.: 27061 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.582 AC: 88485 AN: 152050 Hom.: 27065 Cov.: 32 AF XY: 0.575 AC XY: 42708 AN XY: 74332

African (AFR) AF: 0.393 AC: 16295 AN: 41444

American (AMR) AF: 0.590 AC: 9026 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2212 AN: 3466

East Asian (EAS) AF: 0.528 AC: 2725 AN: 5164

South Asian (SAS) AF: 0.600 AC: 2891 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5716 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47545 AN: 67980

Other (OTH) AF: 0.612 AC: 1288 AN: 2104

Alfa AF: 0.631 Hom.: 9027

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.51
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10132760; hg19: chr14-22196541;