11-118274971-C-T

Variant names:

• chr11-118274971-C-T
• rs17122021

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 0.4 in 151,828 control chromosomes in the GnomAD database, including 12,532 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 0.40 (12532 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.400 AC: 60646 AN: 151710 Hom.: 12522 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.400 AC: 60706 AN: 151828 Hom.: 12532 Cov.: 30 AF XY: 0.401 AC XY: 29724 AN XY: 74194

African (AFR) AF: 0.298 AC: 12315 AN: 41376

American (AMR) AF: 0.401 AC: 6113 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1576 AN: 3464

East Asian (EAS) AF: 0.529 AC: 2721 AN: 5144

South Asian (SAS) AF: 0.490 AC: 2359 AN: 4814

European-Finnish (FIN) AF: 0.468 AC: 4932 AN: 10546

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29368 AN: 67922

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.413 Hom.: 28606

Bravo AF: 0.392

Asia WGS AF: 0.512 AC: 1779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.33
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs17122021; hg19: chr11-118145686;