rs176481

Variant names:

• chr7-106087479-G-A
• rs176481

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.326 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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.344

Alfa AF: 0.360 Hom.: 5470

Bravo AF: 0.319

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs176481; hg19: chr7-105727925;