rs952018

Variant names:

• chr13-105537786-T-C
• rs952018

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 0.393 in 151,984 control chromosomes in the GnomAD database, including 13,018 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 0.39 (13018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 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: 0.393 AC: 59661 AN: 151866 Hom.: 13010 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.393 AC: 59677 AN: 151984 Hom.: 13018 Cov.: 32 AF XY: 0.395 AC XY: 29346 AN XY: 74256

African (AFR) AF: 0.194 AC: 8046 AN: 41488

American (AMR) AF: 0.482 AC: 7353 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3472

East Asian (EAS) AF: 0.433 AC: 2238 AN: 5168

South Asian (SAS) AF: 0.491 AC: 2364 AN: 4812

European-Finnish (FIN) AF: 0.427 AC: 4503 AN: 10544

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32200 AN: 67938

Other (OTH) AF: 0.389 AC: 824 AN: 2116

Alfa AF: 0.423 Hom.: 1924

Bravo AF: 0.385

Asia WGS AF: 0.403 AC: 1401 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.54
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs952018; hg19: chr13-106190135;