rs150892

Positions:

• chr1-96050696-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.96050696C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;