rs17144687

Variant names:

• chr5-118824240-A-C
• rs17144687

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0434 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

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0756

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0293 Hom.: 92

Bravo AF: 0.0441

Asia WGS AF: 0.0250 AC: 85 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17144687; hg19: chr5-118159935;