rs1989858

Variant names:

• chr17-47101958-G-A
• rs1989858

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 0.188 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
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.189 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

African (AFR) AF: 0.0670 AC: 2777 AN: 41452

American (AMR) AF: 0.239 AC: 3651 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2898 AN: 5166

South Asian (SAS) AF: 0.237 AC: 1139 AN: 4814

European-Finnish (FIN) AF: 0.294 AC: 3107 AN: 10552

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14004 AN: 67980

Other (OTH) AF: 0.204 AC: 429 AN: 2108

Alfa AF: 0.193 Hom.: 574

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1989858; hg19: chr17-45179324;