rs17209237

Variant names:

• chr5-143277647-A-G
• rs17209237

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 0.18 in 152,200 control chromosomes in the GnomAD database, including 3,011 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 0.18 (3011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 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: 0.181 AC: 27452 AN: 152082 Hom.: 3010 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.180 AC: 27453 AN: 152200 Hom.: 3011 Cov.: 32 AF XY: 0.179 AC XY: 13354 AN XY: 74418

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.182

Alfa AF: 0.229 Hom.: 7105

Bravo AF: 0.174

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17209237; hg19: chr5-142657212; COSMIC: COSV51541157;