chr11-7946812-C-T

Variant names:

• chr11-7946812-C-T
• rs878860

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 0.357 in 151,928 control chromosomes in the GnomAD database, including 10,531 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 0.36 (10531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 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: 0.357 AC: 54263 AN: 151808 Hom.: 10533 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.357 AC: 54274 AN: 151928 Hom.: 10531 Cov.: 32 AF XY: 0.362 AC XY: 26852 AN XY: 74258

African (AFR) AF: 0.196 AC: 8125 AN: 41424

American (AMR) AF: 0.445 AC: 6800 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2150 AN: 5170

South Asian (SAS) AF: 0.343 AC: 1649 AN: 4812

European-Finnish (FIN) AF: 0.467 AC: 4921 AN: 10542

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27698 AN: 67932

Other (OTH) AF: 0.380 AC: 798 AN: 2100

Alfa AF: 0.393 Hom.: 42061

Bravo AF: 0.348

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.32
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs878860; hg19: chr11-7968359;