rs6945846

Variant names:

• chr7-114762861-T-C
• rs6945846

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 0.143 in 152,142 control chromosomes in the GnomAD database, including 2,234 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 0.14 (2234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 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: 0.143 AC: 21734 AN: 152024 Hom.: 2235 Cov.: 31

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0809

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.143 AC: 21730 AN: 152142 Hom.: 2234 Cov.: 31 AF XY: 0.142 AC XY: 10539 AN XY: 74354

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0809

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.125

Alfa AF: 0.181 Hom.: 387

Bravo AF: 0.127

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6945846; hg19: chr7-114402916;