7-155178759-G-C

Variant names:

• chr7-155178759-G-C
• rs10263087

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 0.844 in 152,090 control chromosomes in the GnomAD database, including 54,786 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 0.84 (54786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 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: 0.844 AC: 128211 AN: 151972 Hom.: 54749 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.844 AC: 128311 AN: 152090 Hom.: 54786 Cov.: 32 AF XY: 0.844 AC XY: 62761 AN XY: 74352

African (AFR) AF: 0.693 AC: 28729 AN: 41430

American (AMR) AF: 0.890 AC: 13615 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3472

East Asian (EAS) AF: 0.821 AC: 4250 AN: 5174

South Asian (SAS) AF: 0.872 AC: 4205 AN: 4820

European-Finnish (FIN) AF: 0.870 AC: 9190 AN: 10566

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.919 AC: 62485 AN: 68016

Other (OTH) AF: 0.860 AC: 1819 AN: 2116

Alfa AF: 0.905 Hom.: 29914

Bravo AF: 0.838

Asia WGS AF: 0.856 AC: 2969 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10263087; hg19: chr7-154970469;