rs2050935

Variant names:

• chr1-203362419-C-T
• rs2050935

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 0.82 in 152,114 control chromosomes in the GnomAD database, including 51,178 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 0.82 (51178 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 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: 0.820 AC: 124626 AN: 151996 Hom.: 51128 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.820 AC: 124732 AN: 152114 Hom.: 51178 Cov.: 31 AF XY: 0.821 AC XY: 61046 AN XY: 74372

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.811

Alfa AF: 0.802 Hom.: 22233

Bravo AF: 0.825

Asia WGS AF: 0.793 AC: 2754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2050935; hg19: chr1-203331547;