rs13202984

Variant names:

• chr6-36613372-A-G
• rs13202984

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 0.246 in 152,178 control chromosomes in the GnomAD database, including 6,141 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 0.25 (6141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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: 0.246 AC: 37439 AN: 152060 Hom.: 6141 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.246 AC: 37436 AN: 152178 Hom.: 6141 Cov.: 32 AF XY: 0.244 AC XY: 18125 AN XY: 74374

African (AFR) AF: 0.0606 AC: 2520 AN: 41566

American (AMR) AF: 0.212 AC: 3235 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3468

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5186

South Asian (SAS) AF: 0.165 AC: 797 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3697 AN: 10558

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25113 AN: 67994

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.326 Hom.: 28955

Bravo AF: 0.227

Asia WGS AF: 0.0900 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs13202984; hg19: chr6-36581149; COSMIC: COSV70615836;