rs4943398

Variant names:

• chr13-36610927-T-A
• rs4943398

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 0.429 in 152,032 control chromosomes in the GnomAD database, including 16,409 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 0.43 (16409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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: 0.429 AC: 65224 AN: 151914 Hom.: 16406 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.429 AC: 65238 AN: 152032 Hom.: 16409 Cov.: 32 AF XY: 0.428 AC XY: 31769 AN XY: 74286

African (AFR) AF: 0.173 AC: 7160 AN: 41480

American (AMR) AF: 0.494 AC: 7534 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1071 AN: 5164

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4812

European-Finnish (FIN) AF: 0.541 AC: 5709 AN: 10560

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38133 AN: 67964

Other (OTH) AF: 0.469 AC: 990 AN: 2112

Alfa AF: 0.487 Hom.: 2426

Bravo AF: 0.415

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.73
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4943398; hg19: chr13-37185064;