rs4950929

chr1-203190998-G-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 0.841 in 152,196 control chromosomes in the GnomAD database, including 54,082 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 0.84 (54082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.840 AC: 127807 AN: 152078 Hom.: 54025 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.841 AC: 127924 AN: 152196 Hom.: 54082 Cov.: 32 AF XY: 0.841 AC XY: 62535 AN XY: 74394

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.852

Alfa AF: 0.829 Hom.: 5043

Bravo AF: 0.856

Asia WGS AF: 0.868 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.16
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4950929; hg19: chr1-203160126;