rs17209237

chr5-143277647-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;