11-118808920-A-T

Variant names:

• chr11-118808920-A-T
• rs1784300

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 0.362 in 151,968 control chromosomes in the GnomAD database, including 10,870 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 (10870 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 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: 0.362 AC: 54994 AN: 151852 Hom.: 10862 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.362 AC: 55037 AN: 151968 Hom.: 10870 Cov.: 31 AF XY: 0.361 AC XY: 26831 AN XY: 74250

African (AFR) AF: 0.215 AC: 8918 AN: 41494

American (AMR) AF: 0.508 AC: 7740 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3468

East Asian (EAS) AF: 0.383 AC: 1982 AN: 5174

South Asian (SAS) AF: 0.197 AC: 948 AN: 4814

European-Finnish (FIN) AF: 0.416 AC: 4380 AN: 10524

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28305 AN: 67928

Other (OTH) AF: 0.391 AC: 826 AN: 2114

Alfa AF: 0.282 Hom.: 881

Bravo AF: 0.369

Asia WGS AF: 0.291 AC: 1013 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1784300; hg19: chr11-118679629;