rs13202984

Positions:

• chr6-36613372-A-G

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 0.246 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.229

Alfa AF: 0.342 Hom.: 13057

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

Splicing

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

Publications

LitVar

Other links and lift over

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