rs6945902

Variant names:

• chr7-12246783-C-A
• rs6945902

Your query was ambiguous. Multiple possible variants found:

• chr7-12246783-C-A
• chr7-12246783-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.618 AC: 25585 AN: 41394

American (AMR) AF: 0.392 AC: 5984 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3462

East Asian (EAS) AF: 0.411 AC: 2122 AN: 5162

South Asian (SAS) AF: 0.391 AC: 1882 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1752 AN: 10420

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14618 AN: 67924

Other (OTH) AF: 0.330 AC: 694 AN: 2106

Alfa AF: 0.255 Hom.: 9107

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
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs6945902; hg19: chr7-12286409;