rs12202350

Variant names:

• chr6-159958064-T-C
• rs12202350

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 0.0619 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0141 AC: 587 AN: 41588

American (AMR) AF: 0.0399 AC: 611 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0860 AC: 298 AN: 3466

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4828

European-Finnish (FIN) AF: 0.0944 AC: 1000 AN: 10592

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6641 AN: 68006

Other (OTH) AF: 0.0583 AC: 123 AN: 2110

Alfa AF: 0.0860 Hom.: 669

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
PhyloP100		-3.4

Splicing

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

Other links and lift over

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