rs4661129

Positions:

• chr1-157353006-C-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 0.107 in 152,198 control chromosomes in the GnomAD database, including 1,166 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 0.11 (1166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16346 AN: 152080 Hom.: 1166 Cov.: 32

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.107 AC: 16347 AN: 152198 Hom.: 1166 Cov.: 32 AF XY: 0.105 AC XY: 7813 AN XY: 74406

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.120

Alfa AF: 0.128 Hom.: 225

Bravo AF: 0.100

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4661129; hg19: chr1-157322796;