11-116182567-G-A

Variant names:

• chr11-116182567-G-A
• rs2251835

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 0.103 in 152,114 control chromosomes in the GnomAD database, including 985 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 0.10 (985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.927
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15638 AN: 151996 Hom.: 983 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0919

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.103 AC: 15648 AN: 152114 Hom.: 985 Cov.: 32 AF XY: 0.104 AC XY: 7705 AN XY: 74354

African (AFR) AF: 0.0511 AC: 2119 AN: 41508

American (AMR) AF: 0.160 AC: 2449 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1487 AN: 5154

South Asian (SAS) AF: 0.0996 AC: 479 AN: 4808

European-Finnish (FIN) AF: 0.0919 AC: 972 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7327 AN: 68002

Other (OTH) AF: 0.122 AC: 258 AN: 2110

Alfa AF: 0.0964 Hom.: 597

Bravo AF: 0.108

Asia WGS AF: 0.182 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.61
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs2251835; hg19: chr11-116053284;