7-130291562-G-T

Position:

• chr7-130291562-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 0.141 in 152,196 control chromosomes in the GnomAD database, including 1,661 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 0.14 (1661 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.130291562G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21415 AN: 152078 Hom.: 1661 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.141 AC: 21419 AN: 152196 Hom.: 1661 Cov.: 31 AF XY: 0.138 AC XY: 10279 AN XY: 74408

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.159

Alfa AF: 0.160 Hom.: 2811

Bravo AF: 0.143

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs901799; hg19: chr7-129931402;