chr7-87118560-A-G

Variant names:

• chr7-87118560-A-G
• rs1859124

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 0.915 in 151,448 control chromosomes in the GnomAD database, including 63,610 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 0.91 (63610 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.915 AC: 138450 AN: 151332 Hom.: 63560 Cov.: 28

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.915 AC: 138554 AN: 151448 Hom.: 63610 Cov.: 28 AF XY: 0.913 AC XY: 67494 AN XY: 73920

African (AFR) AF: 0.981 AC: 40475 AN: 41278

American (AMR) AF: 0.861 AC: 13119 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3165 AN: 3466

East Asian (EAS) AF: 0.735 AC: 3774 AN: 5136

South Asian (SAS) AF: 0.875 AC: 4200 AN: 4802

European-Finnish (FIN) AF: 0.910 AC: 9410 AN: 10346

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61391 AN: 67874

Other (OTH) AF: 0.908 AC: 1909 AN: 2102

Alfa AF: 0.905 Hom.: 15417

Bravo AF: 0.913

Asia WGS AF: 0.794 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.61
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs1859124; hg19: chr7-86747876;