chr7-109291458-C-G

Position:

• chr7-109291458-C-G

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 0.575 in 152,022 control chromosomes in the GnomAD database, including 26,645 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 0.58 (26645 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87369 AN: 151904 Hom.: 26640 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.575 AC: 87416 AN: 152022 Hom.: 26645 Cov.: 33 AF XY: 0.590 AC XY: 43836 AN XY: 74286

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.562

Alfa AF: 0.575 Hom.: 3166

Bravo AF: 0.560

Asia WGS AF: 0.818 AC: 2836 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476471; hg19: chr7-108931515;