rs17028008

Variant names:

• chr4-98732053-A-G
• rs17028008

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 0.182 in 152,186 control chromosomes in the GnomAD database, including 3,053 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 0.18 (3053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.182 AC: 27626 AN: 152066 Hom.: 3033 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.182 AC: 27697 AN: 152186 Hom.: 3053 Cov.: 32 AF XY: 0.186 AC XY: 13858 AN XY: 74408

African (AFR) AF: 0.276 AC: 11442 AN: 41496

American (AMR) AF: 0.222 AC: 3394 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1072 AN: 5166

South Asian (SAS) AF: 0.272 AC: 1313 AN: 4828

European-Finnish (FIN) AF: 0.189 AC: 2000 AN: 10598

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7477 AN: 68016

Other (OTH) AF: 0.179 AC: 378 AN: 2116

Alfa AF: 0.137 Hom.: 1266

Bravo AF: 0.188

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.019
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17028008; hg19: chr4-99653204;