1-159714875-G-T

Variant names:

• chr1-159714875-G-T
• rs3091244

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 0.125 in 151,990 control chromosomes in the GnomAD database, including 1,834 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 0.13 (1834 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.125 AC: 18994 AN: 151872 Hom.: 1826 Cov.: 30

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.125 AC: 19027 AN: 151990 Hom.: 1834 Cov.: 30 AF XY: 0.124 AC XY: 9205 AN XY: 74274

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0652

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.124

Alfa AF: 0.00190 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	0.026
DANN	Benign	0.55

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;