rs17523783

Variant names:

• chr1-169633003-G-T
• rs17523783

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 0.208 in 152,012 control chromosomes in the GnomAD database, including 3,738 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 0.21 (3738 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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: 0.208 AC: 31558 AN: 151894 Hom.: 3737 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.208 AC: 31556 AN: 152012 Hom.: 3738 Cov.: 31 AF XY: 0.202 AC XY: 14991 AN XY: 74304

African (AFR) AF: 0.133 AC: 5527 AN: 41464

American (AMR) AF: 0.179 AC: 2736 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3470

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5162

South Asian (SAS) AF: 0.133 AC: 638 AN: 4812

European-Finnish (FIN) AF: 0.204 AC: 2162 AN: 10592

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18823 AN: 67924

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.226 Hom.: 556

Bravo AF: 0.202

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.41
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs17523783; hg19: chr1-169602241;