rs1150461

Variant names:

• chr5-5911268-A-G
• rs1150461

Your query was ambiguous. Multiple possible variants found:

• chr5-5911268-A-G
• chr5-5911268-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 0.602 in 151,974 control chromosomes in the GnomAD database, including 27,863 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 0.60 (27863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 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: 0.602 AC: 91379 AN: 151858 Hom.: 27834 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.602 AC: 91448 AN: 151974 Hom.: 27863 Cov.: 32 AF XY: 0.609 AC XY: 45198 AN XY: 74270

African (AFR) AF: 0.533 AC: 22080 AN: 41408

American (AMR) AF: 0.676 AC: 10331 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3047 AN: 5168

South Asian (SAS) AF: 0.719 AC: 3465 AN: 4816

European-Finnish (FIN) AF: 0.666 AC: 7029 AN: 10560

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41273 AN: 67958

Other (OTH) AF: 0.642 AC: 1357 AN: 2114

Alfa AF: 0.602 Hom.: 13893

Bravo AF: 0.597

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs1150461; hg19: chr5-5911381;