7-121420119-C-T

Position:

• chr7-121420119-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 0.761 in 152,250 control chromosomes in the GnomAD database, including 49,027 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 0.76 (49027 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

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 (NFE) allele frequency at 95% confidence interval = 0.94 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: 0.761 AC: 115780 AN: 152132 Hom.: 49018 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.761 AC: 115812 AN: 152250 Hom.: 49027 Cov.: 33 AF XY: 0.765 AC XY: 56960 AN XY: 74448

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.790

Alfa AF: 0.844 Hom.: 13996

Bravo AF: 0.731

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2141360; hg19: chr7-121060173;