7-121420119-C-T

Variant names:

• chr7-121420119-C-T
• rs2141360

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 0.761 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.761 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

African (AFR) AF: 0.359 AC: 14906 AN: 41500

American (AMR) AF: 0.802 AC: 12276 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3173 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3842 AN: 5180

South Asian (SAS) AF: 0.854 AC: 4122 AN: 4828

European-Finnish (FIN) AF: 0.969 AC: 10289 AN: 10614

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64403 AN: 68036

Other (OTH) AF: 0.790 AC: 1670 AN: 2114

Alfa AF: 0.818 Hom.: 15179

Bravo AF: 0.731

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.20
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs2141360; hg19: chr7-121060173;