rs176481

Positions:

• chr7-106087479-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;