rs150892

Variant names:

• chr1-96050696-C-T
• rs150892

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 0.424 in 151,962 control chromosomes in the GnomAD database, including 14,762 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 0.42 (14762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 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: 0.425 AC: 64492 AN: 151844 Hom.: 14763 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.424 AC: 64504 AN: 151962 Hom.: 14762 Cov.: 32 AF XY: 0.426 AC XY: 31632 AN XY: 74266

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.0978

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.437

Alfa AF: 0.488 Hom.: 34422

Bravo AF: 0.404

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150892; hg19: chr1-96516252;