rs17034019

Variant names:

• chr4-103726500-G-A
• rs17034019

Your query was ambiguous. Multiple possible variants found:

• chr4-103726500-G-A
• chr4-103726500-G-T

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 0.116 in 152,020 control chromosomes in the GnomAD database, including 1,311 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 0.12 (1311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17565 AN: 151902 Hom.: 1308 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.116 AC: 17579 AN: 152020 Hom.: 1311 Cov.: 32 AF XY: 0.123 AC XY: 9162 AN XY: 74300

African (AFR) AF: 0.100 AC: 4165 AN: 41474

American (AMR) AF: 0.144 AC: 2192 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3468

East Asian (EAS) AF: 0.354 AC: 1827 AN: 5164

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4818

European-Finnish (FIN) AF: 0.133 AC: 1409 AN: 10572

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

European-Non Finnish (NFE) AF: 0.0876 AC: 5954 AN: 67946

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.0976 Hom.: 95

Bravo AF: 0.113

Asia WGS AF: 0.289 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17034019; hg19: chr4-104647657;