5-24855040-G-C

Variant names:

• chr5-24855040-G-C
• rs10043237

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 0.146 in 152,060 control chromosomes in the GnomAD database, including 1,934 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 0.15 (1934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22162 AN: 151942 Hom.: 1929 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.146 AC: 22180 AN: 152060 Hom.: 1934 Cov.: 32 AF XY: 0.153 AC XY: 11343 AN XY: 74326

African (AFR) AF: 0.148 AC: 6157 AN: 41484

American (AMR) AF: 0.162 AC: 2480 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2283 AN: 5132

South Asian (SAS) AF: 0.194 AC: 937 AN: 4820

European-Finnish (FIN) AF: 0.203 AC: 2149 AN: 10576

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7512 AN: 67988

Other (OTH) AF: 0.140 AC: 294 AN: 2106

Alfa AF: 0.0573 Hom.: 52

Bravo AF: 0.145

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10043237; hg19: chr5-24855149;