13-21893850-G-A

Variant names:

• chr13-21893850-G-A
• rs17368525

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 0.459 in 151,820 control chromosomes in the GnomAD database, including 16,413 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 0.46 (16413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69583 AN: 151702 Hom.: 16392 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.459 AC: 69649 AN: 151820 Hom.: 16413 Cov.: 31 AF XY: 0.463 AC XY: 34324 AN XY: 74158

African (AFR) AF: 0.356 AC: 14709 AN: 41352

American (AMR) AF: 0.532 AC: 8117 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.582 AC: 3006 AN: 5168

South Asian (SAS) AF: 0.612 AC: 2940 AN: 4804

European-Finnish (FIN) AF: 0.451 AC: 4738 AN: 10512

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32755 AN: 67946

Other (OTH) AF: 0.482 AC: 1015 AN: 2106

Alfa AF: 0.476 Hom.: 52852

Bravo AF: 0.458

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.29
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs17368525; hg19: chr13-22467989;