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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.116 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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.130

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17034019; hg19: chr4-104647657;