rs4961118

Variant names:

• chr8-89173194-G-T
• rs4961118

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 0.529 in 151,634 control chromosomes in the GnomAD database, including 23,035 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 0.53 (23035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80167 AN: 151516 Hom.: 23033 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.529 AC: 80198 AN: 151634 Hom.: 23035 Cov.: 32 AF XY: 0.529 AC XY: 39185 AN XY: 74102

African (AFR) AF: 0.289 AC: 11967 AN: 41420

American (AMR) AF: 0.611 AC: 9292 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1990 AN: 3460

East Asian (EAS) AF: 0.578 AC: 2966 AN: 5130

South Asian (SAS) AF: 0.541 AC: 2611 AN: 4822

European-Finnish (FIN) AF: 0.560 AC: 5903 AN: 10538

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43498 AN: 67752

Other (OTH) AF: 0.578 AC: 1219 AN: 2108

Alfa AF: 0.610 Hom.: 35264

Bravo AF: 0.522

Asia WGS AF: 0.568 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.65
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4961118; hg19: chr8-90185423;