rs1460277

Variant names:

• chr18-75798575-A-G
• rs1460277

Your query was ambiguous. Multiple possible variants found:

• chr18-75798575-A-G
• chr18-75798575-A-T

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 0.813 in 152,128 control chromosomes in the GnomAD database, including 50,585 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 0.81 (50585 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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: 0.813 AC: 123626 AN: 152010 Hom.: 50523 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.813 AC: 123755 AN: 152128 Hom.: 50585 Cov.: 31 AF XY: 0.811 AC XY: 60322 AN XY: 74356

African (AFR) AF: 0.897 AC: 37238 AN: 41506

American (AMR) AF: 0.753 AC: 11513 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3472

East Asian (EAS) AF: 0.768 AC: 3966 AN: 5166

South Asian (SAS) AF: 0.769 AC: 3709 AN: 4824

European-Finnish (FIN) AF: 0.785 AC: 8285 AN: 10558

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53693 AN: 67992

Other (OTH) AF: 0.800 AC: 1691 AN: 2114

Alfa AF: 0.788 Hom.: 34398

Bravo AF: 0.814

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.29
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1460277; hg19: chr18-73510530;