rs150892

Variant names:

• chr1-96050696-C-T
• rs150892

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.287 AC: 11894 AN: 41464

American (AMR) AF: 0.401 AC: 6127 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.0978 AC: 504 AN: 5154

South Asian (SAS) AF: 0.479 AC: 2308 AN: 4816

European-Finnish (FIN) AF: 0.580 AC: 6114 AN: 10534

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34418 AN: 67942

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.474 Hom.: 50652

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs150892; hg19: chr1-96516252;