11-113514187-C-G

Variant names:

• chr11-113514187-C-G
• rs1984739

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 0.261 in 152,088 control chromosomes in the GnomAD database, including 6,407 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 0.26 (6407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 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: 0.261 AC: 39734 AN: 151970 Hom.: 6412 Cov.: 32

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.261 AC: 39731 AN: 152088 Hom.: 6407 Cov.: 32 AF XY: 0.270 AC XY: 20071 AN XY: 74352

African (AFR) AF: 0.0753 AC: 3128 AN: 41522

American (AMR) AF: 0.220 AC: 3366 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1004 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5166

South Asian (SAS) AF: 0.379 AC: 1823 AN: 4816

European-Finnish (FIN) AF: 0.451 AC: 4762 AN: 10560

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23131 AN: 67968

Other (OTH) AF: 0.255 AC: 538 AN: 2108

Alfa AF: 0.211 Hom.: 588

Bravo AF: 0.231

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.30
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs1984739; hg19: chr11-113384909;