rs1461240

Variant names:

• chr5-153925792-G-A
• rs1461240

Your query was ambiguous. Multiple possible variants found:

• chr5-153925792-G-A
• chr5-153925792-G-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 0.227 in 151,994 control chromosomes in the GnomAD database, including 4,381 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 0.23 (4381 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.227 AC: 34524 AN: 151876 Hom.: 4370 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.227 AC: 34560 AN: 151994 Hom.: 4381 Cov.: 32 AF XY: 0.226 AC XY: 16797 AN XY: 74284

African (AFR) AF: 0.328 AC: 13572 AN: 41402

American (AMR) AF: 0.180 AC: 2746 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3470

East Asian (EAS) AF: 0.0988 AC: 511 AN: 5174

South Asian (SAS) AF: 0.112 AC: 541 AN: 4810

European-Finnish (FIN) AF: 0.269 AC: 2841 AN: 10558

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12743 AN: 67992

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.205 Hom.: 578

Bravo AF: 0.229

Asia WGS AF: 0.127 AC: 440 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	1.8
DANN	Benign	0.63
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1461240; hg19: chr5-153305352;