7-113419590-C-T

Position:

• chr7-113419590-C-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 0.58 in 151,124 control chromosomes in the GnomAD database, including 25,855 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 0.58 (25855 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113419590C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87603 AN: 151006 Hom.: 25822 Cov.: 29

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.580 AC: 87689 AN: 151124 Hom.: 25855 Cov.: 29 AF XY: 0.581 AC XY: 42874 AN XY: 73734

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.598

Alfa AF: 0.552 Hom.: 2787

Bravo AF: 0.585

Asia WGS AF: 0.779 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894673; hg19: chr7-113059645;