rs12202350

chr6-159958064-T-C

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 0.0619 in 152,292 control chromosomes in the GnomAD database, including 419 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 0.062 (419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0957 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: 0.0620 AC: 9434 AN: 152174 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.0860

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0976

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0619 AC: 9431 AN: 152292 Hom.: 419 Cov.: 32 AF XY: 0.0603 AC XY: 4492 AN XY: 74458

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0399

Gnomad4 ASJ AF: 0.0860

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.0977

Gnomad4 OTH AF: 0.0583

Alfa AF: 0.0870 Hom.: 412

Bravo AF: 0.0555

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.0060
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12202350; hg19: chr6-160379096; COSMIC: COSV69631297;