7-120018824-C-T

Variant names:

• chr7-120018824-C-T
• rs6466729

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 0.108 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.0594

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.0488

Gnomad4 FIN AF: 0.00689

Gnomad4 NFE AF: 0.00978

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.0416 Hom.: 226

Bravo AF: 0.122

Asia WGS AF: 0.0780 AC: 271 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6466729; hg19: chr7-119658878;