rs1989858

Positions:

• chr17-47101958-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 0.188 in 151,996 control chromosomes in the GnomAD database, including 3,536 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 (3536 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

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 (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.189 AC: 28645 AN: 151878 Hom.: 3539 Cov.: 31

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.188 AC: 28647 AN: 151996 Hom.: 3536 Cov.: 31 AF XY: 0.195 AC XY: 14466 AN XY: 74284

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.204

Alfa AF: 0.197 Hom.: 573

Bravo AF: 0.185

Asia WGS AF: 0.340 AC: 1182 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	4.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1989858; hg19: chr17-45179324;