chr13-90213292-G-A

Variant names:

• chr13-90213292-G-A
• rs16944141

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 0.075 in 152,108 control chromosomes in the GnomAD database, including 707 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 0.075 (707 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 13 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 = 0.334 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: 0.0750 AC: 11404 AN: 151990 Hom.: 706 Cov.: 33

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0750 AC: 11410 AN: 152108 Hom.: 707 Cov.: 33 AF XY: 0.0769 AC XY: 5720 AN XY: 74362

African (AFR) AF: 0.0648 AC: 2687 AN: 41462

American (AMR) AF: 0.0881 AC: 1346 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1796 AN: 5174

South Asian (SAS) AF: 0.119 AC: 573 AN: 4810

European-Finnish (FIN) AF: 0.0446 AC: 472 AN: 10582

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0619 AC: 4211 AN: 68012

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0691 Hom.: 2054

Bravo AF: 0.0782

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.72
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs16944141; hg19: chr13-90865546; COSMIC: COSV53316680;