rs17051076

Positions:

• chr4-130729712-G-A
• chr4-130729712-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 0.0484 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.130729712G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.0822

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0581 Hom.: 333

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17051076; hg19: chr4-131650867;