rs932231

Variant names:

• chr14-21998645-G-C
• rs932231

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 0.307 in 151,696 control chromosomes in the GnomAD database, including 10,223 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 0.31 (10223 hom., cov: 29)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46521 AN: 151578 Hom.: 10192 Cov.: 29

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.307 AC: 46597 AN: 151696 Hom.: 10223 Cov.: 29 AF XY: 0.297 AC XY: 21994 AN XY: 74150

African (AFR) AF: 0.621 AC: 25650 AN: 41282

American (AMR) AF: 0.194 AC: 2956 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5166

South Asian (SAS) AF: 0.134 AC: 642 AN: 4804

European-Finnish (FIN) AF: 0.119 AC: 1251 AN: 10548

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13541 AN: 67890

Other (OTH) AF: 0.268 AC: 565 AN: 2106

Alfa AF: 0.264 Hom.: 932

Bravo AF: 0.329

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.26
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs932231; hg19: chr14-22466884;