rs17677316

Variant names:

• chr19-10569565-G-A
• rs17677316

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0801 AC: 3327 AN: 41554

American (AMR) AF: 0.193 AC: 2952 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 758 AN: 3468

East Asian (EAS) AF: 0.107 AC: 553 AN: 5164

South Asian (SAS) AF: 0.164 AC: 790 AN: 4814

European-Finnish (FIN) AF: 0.235 AC: 2482 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16869 AN: 67982

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.231 Hom.: 6861

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs17677316; hg19: chr19-10680241;