rs908922

chr1-152482115-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 0.774 in 152,024 control chromosomes in the GnomAD database, including 45,774 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 0.77 (45774 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117495 AN: 151908 Hom.: 45727 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.774 AC: 117597 AN: 152024 Hom.: 45774 Cov.: 30 AF XY: 0.776 AC XY: 57677 AN XY: 74304

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.785

Alfa AF: 0.739 Hom.: 13034

Bravo AF: 0.780

Asia WGS AF: 0.765 AC: 2662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs908922; hg19: chr1-152454591;