rs176481

Variant names:

• chr7-106087479-G-A
• rs176481

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 0.326 in 151,822 control chromosomes in the GnomAD database, including 8,258 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 0.33 (8258 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.326 AC: 49399 AN: 151704 Hom.: 8249 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.326 AC: 49447 AN: 151822 Hom.: 8258 Cov.: 31 AF XY: 0.326 AC XY: 24166 AN XY: 74192

African (AFR) AF: 0.247 AC: 10205 AN: 41374

American (AMR) AF: 0.318 AC: 4854 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2020 AN: 5178

South Asian (SAS) AF: 0.484 AC: 2338 AN: 4826

European-Finnish (FIN) AF: 0.284 AC: 2978 AN: 10472

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24644 AN: 67918

Other (OTH) AF: 0.344 AC: 725 AN: 2106

Alfa AF: 0.350 Hom.: 18249

Bravo AF: 0.319

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.60
DANN	Benign	0.56
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs176481; hg19: chr7-105727925;