rs424950

Variant names:

• chr1-163987266-G-C
• rs424950

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.395 in 151,958 control chromosomes in the GnomAD database, including 13,100 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 0.40 (13100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 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: 0.395 AC: 60019 AN: 151842 Hom.: 13094 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.395 AC: 60046 AN: 151958 Hom.: 13100 Cov.: 32 AF XY: 0.398 AC XY: 29568 AN XY: 74270

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.424

Alfa AF: 0.431 Hom.: 1858

Bravo AF: 0.375

Asia WGS AF: 0.466 AC: 1620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs424950; hg19: chr1-163956503;