chr13-36610927-T-A

Variant names:

• chr13-36610927-T-A
• rs4943398

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.469

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943398; hg19: chr13-37185064;