1-155159197-A-G

Variant names:

• chr1-155159197-A-G
• rs4276913

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 0.393 in 152,086 control chromosomes in the GnomAD database, including 12,870 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 0.39 (12870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 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: 0.393 AC: 59763 AN: 151968 Hom.: 12874 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.393 AC: 59770 AN: 152086 Hom.: 12870 Cov.: 32 AF XY: 0.400 AC XY: 29741 AN XY: 74308

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.385

Alfa AF: 0.403 Hom.: 12314

Bravo AF: 0.396

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4276913; hg19: chr1-155131673;