rs4656241

Variant names:

• chr1-159644196-T-C
• rs4656241

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.130 AC: 5392 AN: 41498

American (AMR) AF: 0.264 AC: 4039 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3470

East Asian (EAS) AF: 0.0188 AC: 97 AN: 5172

South Asian (SAS) AF: 0.121 AC: 584 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2258 AN: 10570

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14518 AN: 67986

Other (OTH) AF: 0.221 AC: 465 AN: 2108

Alfa AF: 0.208 Hom.: 1930

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4656241; hg19: chr1-159613986;