rs17034020

Variant names:

• chr4-103729516-G-A
• rs17034020

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 0.0937 in 152,020 control chromosomes in the GnomAD database, including 1,082 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 0.094 (1082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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: 0.0936 AC: 14222 AN: 151902 Hom.: 1079 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0937 AC: 14246 AN: 152020 Hom.: 1082 Cov.: 32 AF XY: 0.0893 AC XY: 6635 AN XY: 74334

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0301

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0537

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0593 Hom.: 426

Bravo AF: 0.101

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17034020; hg19: chr4-104650673;