rs2050935

chr1-203362419-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 0.82 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;