rs1040924

Variant names:

• chr5-158045337-A-G
• rs1040924

Your query was ambiguous. Multiple possible variants found:

• chr5-158045337-A-G
• chr5-158045337-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 0.559 in 151,880 control chromosomes in the GnomAD database, including 24,823 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 0.56 (24823 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84875 AN: 151760 Hom.: 24792 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.559 AC: 84949 AN: 151880 Hom.: 24823 Cov.: 31 AF XY: 0.553 AC XY: 41077 AN XY: 74232

African (AFR) AF: 0.700 AC: 28989 AN: 41410

American (AMR) AF: 0.513 AC: 7827 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3468

East Asian (EAS) AF: 0.177 AC: 915 AN: 5166

South Asian (SAS) AF: 0.378 AC: 1817 AN: 4804

European-Finnish (FIN) AF: 0.529 AC: 5581 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36295 AN: 67908

Other (OTH) AF: 0.519 AC: 1093 AN: 2104

Alfa AF: 0.551 Hom.: 2978

Bravo AF: 0.563

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
DANN	Benign	0.75
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1040924; hg19: chr5-157472345;