7-128930688-T-C

Variant names:

• chr7-128930688-T-C
• rs2402940

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 0.751 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.751 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

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.755

Alfa AF: 0.771 Hom.: 5388

Bravo AF: 0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2402940; hg19: chr7-128570742;