7-11845056-G-T

Variant names:

• chr7-11845056-G-T
• rs6942789

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 0.692 in 152,040 control chromosomes in the GnomAD database, including 36,605 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 0.69 (36605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105058 AN: 151920 Hom.: 36557 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.692 AC: 105166 AN: 152040 Hom.: 36605 Cov.: 32 AF XY: 0.698 AC XY: 51886 AN XY: 74324

African (AFR) AF: 0.730 AC: 30281 AN: 41484

American (AMR) AF: 0.759 AC: 11590 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4184 AN: 5158

South Asian (SAS) AF: 0.646 AC: 3110 AN: 4814

European-Finnish (FIN) AF: 0.746 AC: 7877 AN: 10562

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43469 AN: 67962

Other (OTH) AF: 0.679 AC: 1428 AN: 2102

Alfa AF: 0.659 Hom.: 101858

Bravo AF: 0.697

Asia WGS AF: 0.733 AC: 2547 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.65
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6942789; hg19: chr7-11884682;