7-132003793-T-C

Position:

• chr7-132003793-T-C

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 0.867 in 152,202 control chromosomes in the GnomAD database, including 57,461 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 0.87 (57461 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132003793T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131882 AN: 152084 Hom.: 57399 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.867 AC: 132007 AN: 152202 Hom.: 57461 Cov.: 32 AF XY: 0.869 AC XY: 64615 AN XY: 74398

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.854

Alfa AF: 0.831 Hom.: 40556

Bravo AF: 0.871

Asia WGS AF: 0.938 AC: 3261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.081
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11767564; hg19: chr7-131688552;