7-114083210-C-T

Variant names:

• chr7-114083210-C-T
• rs10447760

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0425 AC: 1765 AN: 41554

American (AMR) AF: 0.154 AC: 2362 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.0156 AC: 81 AN: 5182

South Asian (SAS) AF: 0.104 AC: 500 AN: 4824

European-Finnish (FIN) AF: 0.244 AC: 2585 AN: 10592

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17307 AN: 67998

Other (OTH) AF: 0.183 AC: 388 AN: 2116

Alfa AF: 0.230 Hom.: 3777

Bravo AF: 0.158

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.92
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10447760; hg19: chr7-113723265;