7-140443720-C-T

Variant names:

• chr7-140443720-C-T
• rs10952668

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 0.528 in 150,300 control chromosomes in the GnomAD database, including 22,628 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 0.53 (22628 hom., cov: 27)
• Consequence: LOC642355 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 3 publications found

Genes affected

LOC642355 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.528 AC: 79268 AN: 150180 Hom.: 22584 Cov.: 27

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.528 AC: 79362 AN: 150300 Hom.: 22628 Cov.: 27 AF XY: 0.523 AC XY: 38326 AN XY: 73306

African (AFR) AF: 0.758 AC: 30990 AN: 40910

American (AMR) AF: 0.366 AC: 5476 AN: 14948

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3464

East Asian (EAS) AF: 0.470 AC: 2378 AN: 5062

South Asian (SAS) AF: 0.399 AC: 1891 AN: 4744

European-Finnish (FIN) AF: 0.491 AC: 5003 AN: 10186

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30492 AN: 67714

Other (OTH) AF: 0.487 AC: 1010 AN: 2074

Alfa AF: 0.467 Hom.: 9155

Bravo AF: 0.528

Asia WGS AF: 0.411 AC: 1424 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.41
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10952668; hg19: chr7-140143520; COSMIC: COSV64791297;