11-88249834-T-G

Variant names:

• chr11-88249834-T-G
• rs17754282

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 0.164 in 152,238 control chromosomes in the GnomAD database, including 2,334 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 0.16 (2334 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.252 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: 0.164 AC: 24881 AN: 152120 Hom.: 2328 Cov.: 33

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.164 AC: 24894 AN: 152238 Hom.: 2334 Cov.: 33 AF XY: 0.168 AC XY: 12479 AN XY: 74424

African (AFR) AF: 0.0943 AC: 3918 AN: 41548

American (AMR) AF: 0.259 AC: 3958 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.178 AC: 921 AN: 5184

South Asian (SAS) AF: 0.206 AC: 994 AN: 4826

European-Finnish (FIN) AF: 0.198 AC: 2101 AN: 10596

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12053 AN: 68010

Other (OTH) AF: 0.158 AC: 333 AN: 2108

Alfa AF: 0.173 Hom.: 4343

Bravo AF: 0.165

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17754282; hg19: chr11-87983002;