13-21623771-T-C

Variant names:

• chr13-21623771-T-C
• rs264729

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 0.484 in 152,032 control chromosomes in the GnomAD database, including 18,803 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 0.48 (18803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.623 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: 0.484 AC: 73456 AN: 151914 Hom.: 18757 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.484 AC: 73567 AN: 152032 Hom.: 18803 Cov.: 32 AF XY: 0.492 AC XY: 36569 AN XY: 74318

African (AFR) AF: 0.629 AC: 26103 AN: 41468

American (AMR) AF: 0.492 AC: 7517 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3147 AN: 5160

South Asian (SAS) AF: 0.538 AC: 2586 AN: 4804

European-Finnish (FIN) AF: 0.466 AC: 4929 AN: 10566

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26672 AN: 67966

Other (OTH) AF: 0.469 AC: 988 AN: 2108

Alfa AF: 0.426 Hom.: 53308

Bravo AF: 0.490

Asia WGS AF: 0.582 AC: 2022 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	0.30
DANN	Benign	0.68
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs264729; hg19: chr13-22197910;