7-128930688-T-C

Variant names:

• chr7-128930688-T-C
• rs2402940

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 0.751 in 149,636 control chromosomes in the GnomAD database, including 43,162 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 0.75 (43162 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 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: 0.751 AC: 112282 AN: 149514 Hom.: 43156 Cov.: 25

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.751 AC: 112330 AN: 149636 Hom.: 43162 Cov.: 25 AF XY: 0.750 AC XY: 54628 AN XY: 72842

African (AFR) AF: 0.620 AC: 25328 AN: 40834

American (AMR) AF: 0.660 AC: 9959 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3046 AN: 3446

East Asian (EAS) AF: 0.598 AC: 3035 AN: 5074

South Asian (SAS) AF: 0.833 AC: 3940 AN: 4732

European-Finnish (FIN) AF: 0.859 AC: 8349 AN: 9720

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.830 AC: 56034 AN: 67474

Other (OTH) AF: 0.755 AC: 1567 AN: 2076

Alfa AF: 0.771 Hom.: 5388

Bravo AF: 0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.52
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2402940; hg19: chr7-128570742;