chr7-120018824-C-T

Variant names:

• chr7-120018824-C-T
• rs6466729

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 0.108 in 151,524 control chromosomes in the GnomAD database, including 2,512 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 0.11 (2512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.107 AC: 16264 AN: 151406 Hom.: 2503 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.00689

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00978

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.108 AC: 16309 AN: 151524 Hom.: 2512 Cov.: 32 AF XY: 0.105 AC XY: 7780 AN XY: 74056

African (AFR) AF: 0.336 AC: 13873 AN: 41270

American (AMR) AF: 0.0594 AC: 903 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0205 AC: 71 AN: 3456

East Asian (EAS) AF: 0.0526 AC: 272 AN: 5170

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4820

European-Finnish (FIN) AF: 0.00689 AC: 73 AN: 10588

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.00978 AC: 662 AN: 67710

Other (OTH) AF: 0.0928 AC: 195 AN: 2102

Alfa AF: 0.0513 Hom.: 465

Bravo AF: 0.122

Asia WGS AF: 0.0780 AC: 271 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.11
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6466729; hg19: chr7-119658878;