rs17677316

Positions:

• chr19-10569565-G-A

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 0.187 in 152,156 control chromosomes in the GnomAD database, including 3,143 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 (3143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

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 (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28383 AN: 152038 Hom.: 3142 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.187 AC: 28396 AN: 152156 Hom.: 3143 Cov.: 32 AF XY: 0.184 AC XY: 13710 AN XY: 74358

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.202

Alfa AF: 0.237 Hom.: 5582

Bravo AF: 0.179

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17677316; hg19: chr19-10680241;