1-159685936-G-T

Variant names:

• chr1-159685936-G-T
• rs2592902

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 0.357 in 152,030 control chromosomes in the GnomAD database, including 10,215 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 0.36 (10215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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: 0.358 AC: 54324 AN: 151912 Hom.: 10209 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.357 AC: 54350 AN: 152030 Hom.: 10215 Cov.: 32 AF XY: 0.360 AC XY: 26732 AN XY: 74312

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.369

Alfa AF: 0.366 Hom.: 1269

Bravo AF: 0.354

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.8
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2592902; hg19: chr1-159655726;