7-130773172-C-G

Position:

• chr7-130773172-C-G

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 0.548 in 151,716 control chromosomes in the GnomAD database, including 24,311 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 0.55 (24311 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

(HGNC:):

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 = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.130773172C>G		intergenic_region
LOC105375508	XR_007060527.1	n.179-9648C>G		intron_variant
LOC105375508	XR_927976.3	n.179-9648C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83075 AN: 151594 Hom.: 24267 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.548 AC: 83167 AN: 151716 Hom.: 24311 Cov.: 32 AF XY: 0.551 AC XY: 40872 AN XY: 74128

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.522

Alfa AF: 0.299 Hom.: 652

Bravo AF: 0.569

Asia WGS AF: 0.587 AC: 2023 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.60
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562398; hg19: chr7-130457931;