rs2369146

Variant names:

• chr1-159698405-A-G
• rs2369146

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 0.738 in 152,018 control chromosomes in the GnomAD database, including 41,826 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 0.74 (41826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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: 0.738 AC: 112063 AN: 151900 Hom.: 41806 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.738 AC: 112128 AN: 152018 Hom.: 41826 Cov.: 32 AF XY: 0.740 AC XY: 54961 AN XY: 74292

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.762

Alfa AF: 0.769 Hom.: 90934

Bravo AF: 0.733

Asia WGS AF: 0.725 AC: 2518 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2369146; hg19: chr1-159668195;