rs238281

Variant names:

• chr13-42336746-T-C
• rs238281

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 0.672 in 152,096 control chromosomes in the GnomAD database, including 34,521 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 0.67 (34521 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845
• Publications: 7 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 = 0.768 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: 0.672 AC: 102122 AN: 151978 Hom.: 34497 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.672 AC: 102198 AN: 152096 Hom.: 34521 Cov.: 33 AF XY: 0.670 AC XY: 49809 AN XY: 74332

African (AFR) AF: 0.683 AC: 28345 AN: 41482

American (AMR) AF: 0.685 AC: 10479 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.788 AC: 4083 AN: 5180

South Asian (SAS) AF: 0.707 AC: 3403 AN: 4816

European-Finnish (FIN) AF: 0.598 AC: 6310 AN: 10560

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44606 AN: 67970

Other (OTH) AF: 0.710 AC: 1501 AN: 2114

Alfa AF: 0.672 Hom.: 44857

Bravo AF: 0.681

Asia WGS AF: 0.715 AC: 2487 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	0.39
DANN	Benign	0.27
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs238281; hg19: chr13-42910882; COSMIC: COSV69348092;