chr13-21911876-T-G

Variant names:

• chr13-21911876-T-G
• rs7338014

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 0.322 in 151,788 control chromosomes in the GnomAD database, including 8,426 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 0.32 (8426 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 2 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48750 AN: 151670 Hom.: 8407 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.322 AC: 48818 AN: 151788 Hom.: 8426 Cov.: 31 AF XY: 0.328 AC XY: 24313 AN XY: 74156

African (AFR) AF: 0.415 AC: 17167 AN: 41360

American (AMR) AF: 0.338 AC: 5161 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2405 AN: 5124

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4804

European-Finnish (FIN) AF: 0.365 AC: 3835 AN: 10498

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16848 AN: 67950

Other (OTH) AF: 0.308 AC: 651 AN: 2116

Alfa AF: 0.268 Hom.: 2966

Bravo AF: 0.326

Asia WGS AF: 0.341 AC: 1185 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	4.1
DANN	Benign	0.46
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7338014; hg19: chr13-22486015;