rs6945846

chr7-114762861-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;