rs11699291

Variant names:

• chr20-48268200-G-A
• rs11699291
• ENST00000668815.1:n.116-2675C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000668815.1(ENSG00000288083):​n.116-2675C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0455 in 152,258 control chromosomes in the GnomAD database, including 201 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 0.045 (201 hom., cov: 33)
• Consequence: ENSG00000288083 ENST00000668815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

Genes affected

ENSG00000288083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0455 (6922/152258) while in subpopulation EAS AF = 0.0526 (273/5186). AF 95% confidence interval is 0.0477. There are 201 homozygotes in GnomAd4. There are 3361 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 201 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668815.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288083	ENST00000668815.1		n.116-2675C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6916 AN: 152142 Hom.: 201 Cov.: 33

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0455 AC: 6922 AN: 152258 Hom.: 201 Cov.: 33 AF XY: 0.0452 AC XY: 3361 AN XY: 74436

African (AFR) AF: 0.0438 AC: 1820 AN: 41552

American (AMR) AF: 0.0384 AC: 587 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3472

East Asian (EAS) AF: 0.0526 AC: 273 AN: 5186

South Asian (SAS) AF: 0.0459 AC: 221 AN: 4810

European-Finnish (FIN) AF: 0.0389 AC: 412 AN: 10598

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3337 AN: 68020

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0449 Hom.: 26

Bravo AF: 0.0454

Asia WGS AF: 0.0490 AC: 171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11699291; hg19: chr20-46896943;