rs679830

Positions:

• chr7-54607180-T-C
• chr7-54607180-T-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 0.882 in 152,082 control chromosomes in the GnomAD database, including 59,714 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 0.88 (59714 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.942 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: 0.883 AC: 134129 AN: 151962 Hom.: 59692 Cov.: 30

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.882 AC: 134208 AN: 152082 Hom.: 59714 Cov.: 30 AF XY: 0.881 AC XY: 65497 AN XY: 74334

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.948

Gnomad4 OTH AF: 0.906

Alfa AF: 0.938 Hom.: 62833

Bravo AF: 0.874

Asia WGS AF: 0.868 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.022
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679830; hg19: chr7-54674873;