rs13218732

Variant names:

• chr6-152944075-A-C
• rs13218732

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 0.0327 in 152,268 control chromosomes in the GnomAD database, including 82 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 0.033 (82 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0777 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: 0.0327 AC: 4979 AN: 152150 Hom.: 82 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0327 AC: 4985 AN: 152268 Hom.: 82 Cov.: 33 AF XY: 0.0326 AC XY: 2425 AN XY: 74456

African (AFR) AF: 0.0232 AC: 963 AN: 41580

American (AMR) AF: 0.0346 AC: 529 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3472

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5184

South Asian (SAS) AF: 0.0845 AC: 407 AN: 4818

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0397 AC: 2696 AN: 67992

Other (OTH) AF: 0.0483 AC: 102 AN: 2112

Alfa AF: 0.0374 Hom.: 13

Bravo AF: 0.0322

Asia WGS AF: 0.0560 AC: 195 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.57
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs13218732; hg19: chr6-153265210;