chr14-21998645-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.21998645G>C		intragenic_variant

Ensembl

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

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 v4.3

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;