rs679830

Variant names:

• chr7-54607180-T-C
• rs679830

Your query was ambiguous. Multiple possible variants found:

• chr7-54607180-T-C
• chr7-54607180-T-G

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 0.882 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.757 AC: 31377 AN: 41436

American (AMR) AF: 0.878 AC: 13413 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3261 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4179 AN: 5164

South Asian (SAS) AF: 0.926 AC: 4460 AN: 4818

European-Finnish (FIN) AF: 0.945 AC: 10001 AN: 10580

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64475 AN: 68022

Other (OTH) AF: 0.906 AC: 1909 AN: 2108

Alfa AF: 0.925 Hom.: 159730

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs679830; hg19: chr7-54674873;