rs17051076

Variant names:

• chr4-130729712-G-A
• rs17051076

Your query was ambiguous. Multiple possible variants found:

• chr4-130729712-G-A
• chr4-130729712-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 0.0484 in 152,184 control chromosomes in the GnomAD database, including 239 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 0.048 (239 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0884 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: 0.0485 AC: 7368 AN: 152064 Hom.: 241 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0484 AC: 7362 AN: 152184 Hom.: 239 Cov.: 33 AF XY: 0.0501 AC XY: 3727 AN XY: 74386

African (AFR) AF: 0.0120 AC: 498 AN: 41548

American (AMR) AF: 0.0316 AC: 483 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.0954 AC: 493 AN: 5170

South Asian (SAS) AF: 0.0822 AC: 396 AN: 4820

European-Finnish (FIN) AF: 0.0781 AC: 827 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4308 AN: 68010

Other (OTH) AF: 0.0441 AC: 93 AN: 2110

Alfa AF: 0.0561 Hom.: 398

Bravo AF: 0.0426

Asia WGS AF: 0.0620 AC: 213 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.1
DANN	Benign	0.85
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17051076; hg19: chr4-131650867;