rs7800687

Variant names:

• chr7-128953665-C-G
• rs7800687

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 0.637 in 152,066 control chromosomes in the GnomAD database, including 31,167 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 0.64 (31167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 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: 0.637 AC: 96785 AN: 151948 Hom.: 31139 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.637 AC: 96857 AN: 152066 Hom.: 31167 Cov.: 32 AF XY: 0.638 AC XY: 47436 AN XY: 74350

African (AFR) AF: 0.594 AC: 24619 AN: 41470

American (AMR) AF: 0.564 AC: 8617 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2622 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2898 AN: 5182

South Asian (SAS) AF: 0.689 AC: 3320 AN: 4816

European-Finnish (FIN) AF: 0.735 AC: 7772 AN: 10574

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44821 AN: 67964

Other (OTH) AF: 0.647 AC: 1369 AN: 2116

Alfa AF: 0.647 Hom.: 3999

Bravo AF: 0.623

Asia WGS AF: 0.629 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.30
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs7800687; hg19: chr7-128593719;