rs6945902

chr7-12246783-C-Achr7-12246783-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 0.355 in 151,740 control chromosomes in the GnomAD database, including 12,052 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 0.35 (12052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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: 0.354 AC: 53731 AN: 151624 Hom.: 12027 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.355 AC: 53818 AN: 151740 Hom.: 12052 Cov.: 31 AF XY: 0.356 AC XY: 26395 AN XY: 74142

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.330

Alfa AF: 0.250 Hom.: 7355

Bravo AF: 0.384

Asia WGS AF: 0.412 AC: 1425 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.18
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6945902; hg19: chr7-12286409;