5-118824240-A-C

Variant names:

• chr5-118824240-A-C
• rs17144687

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 0.0435 in 152,116 control chromosomes in the GnomAD database, including 163 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 0.043 (163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.931
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0434 AC: 6604 AN: 151998 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0435 AC: 6616 AN: 152116 Hom.: 163 Cov.: 32 AF XY: 0.0454 AC XY: 3377 AN XY: 74344

African (AFR) AF: 0.0670 AC: 2779 AN: 41490

American (AMR) AF: 0.0492 AC: 751 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3468

East Asian (EAS) AF: 0.0290 AC: 150 AN: 5166

South Asian (SAS) AF: 0.0187 AC: 90 AN: 4822

European-Finnish (FIN) AF: 0.0756 AC: 801 AN: 10592

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1812 AN: 68008

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0314 Hom.: 140

Bravo AF: 0.0441

Asia WGS AF: 0.0250 AC: 85 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.72
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs17144687; hg19: chr5-118159935;