rs7966506

chr12-94689598-C-T

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 0.465 in 151,936 control chromosomes in the GnomAD database, including 16,601 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 (16601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.465 AC: 70588 AN: 151818 Hom.: 16580 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.465 AC: 70645 AN: 151936 Hom.: 16601 Cov.: 32 AF XY: 0.461 AC XY: 34261 AN XY: 74244

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.454

Alfa AF: 0.475 Hom.: 29702

Bravo AF: 0.458

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.13
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7966506; hg19: chr12-95083374;