rs7966378

Variant names:

• chr12-94689500-C-G
• rs7966378

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 0.402 in 151,566 control chromosomes in the GnomAD database, including 12,390 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 0.40 (12390 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 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: 0.402 AC: 60919 AN: 151448 Hom.: 12367 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.402 AC: 60979 AN: 151566 Hom.: 12390 Cov.: 31 AF XY: 0.400 AC XY: 29600 AN XY: 74044

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.401

Alfa AF: 0.411 Hom.: 1573

Bravo AF: 0.400

Asia WGS AF: 0.367 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7966378; hg19: chr12-95083276;