rs4656241

chr1-159644196-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 0.187 in 152,100 control chromosomes in the GnomAD database, including 2,907 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 0.19 (2907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 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: 0.187 AC: 28496 AN: 151982 Hom.: 2907 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.187 AC: 28516 AN: 152100 Hom.: 2907 Cov.: 32 AF XY: 0.188 AC XY: 13997 AN XY: 74356

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.0188

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.221

Alfa AF: 0.209 Hom.: 1746

Bravo AF: 0.192

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4656241; hg19: chr1-159613986;