rs976906

Variant names:

• chr17-12664783-G-A
• rs976906

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 0.461 in 151,996 control chromosomes in the GnomAD database, including 16,375 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 0.46 (16375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 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: 0.461 AC: 69973 AN: 151878 Hom.: 16358 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.461 AC: 70039 AN: 151996 Hom.: 16375 Cov.: 32 AF XY: 0.460 AC XY: 34155 AN XY: 74268

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.473

Alfa AF: 0.469 Hom.: 4282

Bravo AF: 0.457

Asia WGS AF: 0.431 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs976906; hg19: chr17-12568100;