rs17562083

Variant names:

• chr5-170085744-C-A
• rs17562083

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 0.258 in 152,090 control chromosomes in the GnomAD database, including 6,367 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 0.26 (6367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.259 AC: 39297 AN: 151972 Hom.: 6359 Cov.: 32

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.258 AC: 39312 AN: 152090 Hom.: 6367 Cov.: 32 AF XY: 0.255 AC XY: 18976 AN XY: 74332

Gnomad4 AFR AF: 0.0714

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.284

Alfa AF: 0.338 Hom.: 12399

Bravo AF: 0.248

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.060
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17562083; hg19: chr5-169512748;