7-140443720-C-T

Position:

• chr7-140443720-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 0.528 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.487

Alfa AF: 0.461 Hom.: 7544

Bravo AF: 0.528

Asia WGS AF: 0.411 AC: 1424 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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