rs12663356

chr6-21430497-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 0.516 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.503

Alfa AF: 0.526 Hom.: 12362

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12663356; hg19: chr6-21430728;