rs17470137

Variant names:

• chr5-123195653-G-A
• rs17470137

Your query was ambiguous. Multiple possible variants found:

• chr5-123195653-G-A
• chr5-123195653-G-T

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 0.194 in 152,132 control chromosomes in the GnomAD database, including 3,689 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 0.19 (3689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.194 AC: 29542 AN: 152014 Hom.: 3688 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.194 AC: 29542 AN: 152132 Hom.: 3689 Cov.: 32 AF XY: 0.193 AC XY: 14352 AN XY: 74350

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.200

Alfa AF: 0.243 Hom.: 5857

Bravo AF: 0.180

Asia WGS AF: 0.0610 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17470137; hg19: chr5-122531347;