rs951530

chr4-124863005-T-C

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 0.357 in 152,008 control chromosomes in the GnomAD database, including 10,790 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 0.36 (10790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

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 (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.357 AC: 54169 AN: 151890 Hom.: 10790 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.357 AC: 54191 AN: 152008 Hom.: 10790 Cov.: 32 AF XY: 0.365 AC XY: 27112 AN XY: 74308

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.351

Alfa AF: 0.396 Hom.: 6701

Bravo AF: 0.348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.23
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951530; hg19: chr4-125784160;