rs12663356

Variant names:

• chr6-21430497-T-C
• rs12663356

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 0.516 in 151,742 control chromosomes in the GnomAD database, including 20,541 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 0.52 (20541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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: 0.516 AC: 78274 AN: 151622 Hom.: 20531 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.516 AC: 78318 AN: 151742 Hom.: 20541 Cov.: 32 AF XY: 0.511 AC XY: 37915 AN XY: 74138

African (AFR) AF: 0.531 AC: 21964 AN: 41364

American (AMR) AF: 0.516 AC: 7872 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3466

East Asian (EAS) AF: 0.325 AC: 1678 AN: 5162

South Asian (SAS) AF: 0.445 AC: 2143 AN: 4812

European-Finnish (FIN) AF: 0.498 AC: 5221 AN: 10492

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35750 AN: 67884

Other (OTH) AF: 0.503 AC: 1059 AN: 2106

Alfa AF: 0.522 Hom.: 49563

Bravo AF: 0.522

Asia WGS AF: 0.365 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.68
DANN	Benign	0.57
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12663356; hg19: chr6-21430728;