7-128933074-T-C

Variant names:

• chr7-128933074-T-C
• rs11768806

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 0.736 in 152,214 control chromosomes in the GnomAD database, including 42,572 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 0.74 (42572 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 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: 0.736 AC: 111962 AN: 152096 Hom.: 42567 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.736 AC: 112001 AN: 152214 Hom.: 42572 Cov.: 33 AF XY: 0.737 AC XY: 54822 AN XY: 74420

African (AFR) AF: 0.567 AC: 23558 AN: 41520

American (AMR) AF: 0.657 AC: 10045 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3053 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3098 AN: 5168

South Asian (SAS) AF: 0.826 AC: 3991 AN: 4830

European-Finnish (FIN) AF: 0.864 AC: 9166 AN: 10608

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56449 AN: 68006

Other (OTH) AF: 0.742 AC: 1568 AN: 2114

Alfa AF: 0.764 Hom.: 12702

Bravo AF: 0.711

Asia WGS AF: 0.706 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs11768806; hg19: chr7-128573128;