rs3091244

Positions:

• chr1-159714875-G-A
• chr1-159714875-G-T

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 0.3 in 151,984 control chromosomes in the GnomAD database, including 7,034 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 0.30 (7034 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 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: 0.300 AC: 45553 AN: 151866 Hom.: 7036 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.300 AC: 45581 AN: 151984 Hom.: 7034 Cov.: 30 AF XY: 0.299 AC XY: 22217 AN XY: 74276

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.292

Alfa AF: 0.368 Hom.: 8752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3091244; hg19: chr1-159684665;