rs1811472

Variant names:

• chr1-159672559-G-C
• rs1811472

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 0.395 in 152,066 control chromosomes in the GnomAD database, including 12,606 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 0.40 (12606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

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 (EAS) allele frequency at 95% confidence interval = 0.763 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: 0.395 AC: 60092 AN: 151948 Hom.: 12602 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.395 AC: 60119 AN: 152066 Hom.: 12606 Cov.: 32 AF XY: 0.398 AC XY: 29591 AN XY: 74364

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.399

Alfa AF: 0.389 Hom.: 1649

Bravo AF: 0.399

Asia WGS AF: 0.569 AC: 1977 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	0.091
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1811472; hg19: chr1-159642349;