7-113419590-C-T

Variant names:

• chr7-113419590-C-T
• rs2894673

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;