rs4131568

Variant names:

• chr1-159752266-C-T
• rs4131568

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 0.265 in 152,052 control chromosomes in the GnomAD database, including 6,741 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 0.26 (6741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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: 0.265 AC: 40229 AN: 151934 Hom.: 6738 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.265 AC: 40245 AN: 152052 Hom.: 6741 Cov.: 32 AF XY: 0.272 AC XY: 20178 AN XY: 74314

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.269

Alfa AF: 0.322 Hom.: 4281

Bravo AF: 0.249

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131568; hg19: chr1-159722056;