rs1924966

Variant names:

• chr13-72432915-T-G
• rs1924966

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 0.332 in 151,806 control chromosomes in the GnomAD database, including 9,167 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 0.33 (9167 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50415 AN: 151688 Hom.: 9166 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.332 AC: 50434 AN: 151806 Hom.: 9167 Cov.: 31 AF XY: 0.332 AC XY: 24643 AN XY: 74174

African (AFR) AF: 0.181 AC: 7525 AN: 41474

American (AMR) AF: 0.264 AC: 4003 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2252 AN: 5130

South Asian (SAS) AF: 0.416 AC: 2002 AN: 4818

European-Finnish (FIN) AF: 0.425 AC: 4478 AN: 10528

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27599 AN: 67886

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.388 Hom.: 12650

Bravo AF: 0.310

Asia WGS AF: 0.413 AC: 1433 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.60
DANN	Benign	0.63
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1924966; hg19: chr13-73007053;