7-114083210-C-T

Variant names:

• chr7-114083210-C-T
• rs10447760

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 0.172 in 152,240 control chromosomes in the GnomAD database, including 3,023 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 0.17 (3023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.172 AC: 26155 AN: 152122 Hom.: 3024 Cov.: 33

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.172 AC: 26140 AN: 152240 Hom.: 3023 Cov.: 33 AF XY: 0.170 AC XY: 12646 AN XY: 74412

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.183

Alfa AF: 0.226 Hom.: 2626

Bravo AF: 0.158

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10447760; hg19: chr7-113723265;