rs17834666

Variant names:

• chr4-180308047-G-A
• rs17834666

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 0.132 in 151,986 control chromosomes in the GnomAD database, including 1,397 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 0.13 (1397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.132 AC: 20023 AN: 151866 Hom.: 1400 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.132 AC: 20017 AN: 151986 Hom.: 1397 Cov.: 32 AF XY: 0.132 AC XY: 9778 AN XY: 74250

African (AFR) AF: 0.121 AC: 5021 AN: 41484

American (AMR) AF: 0.118 AC: 1797 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5160

South Asian (SAS) AF: 0.120 AC: 579 AN: 4810

European-Finnish (FIN) AF: 0.166 AC: 1749 AN: 10536

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

European-Non Finnish (NFE) AF: 0.133 AC: 9017 AN: 67958

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.135 Hom.: 2785

Bravo AF: 0.129

Asia WGS AF: 0.158 AC: 547 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17834666; hg19: chr4-181229200;