rs11699311

Variant names:

• chr20-53738792-T-A
• rs11699311
• ENST00000663196.1:n.65T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663196.1(ENSG00000287886):​n.65T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 152,184 control chromosomes in the GnomAD database, including 162 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 0.037 (162 hom., cov: 32)
• Consequence: ENSG00000287886 ENST00000663196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 2 publications found

Genes affected

ENSG00000287886 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904933	XR_007067660.1	n.2030T>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287886	ENST00000663196.1	n.65T>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000293654	ENST00000716917.1	n.504-1612T>A		intron_variant	Intron 2 of 2
ENSG00000293654	ENST00000716918.1	n.340-1612T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5568 AN: 152066 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.00819

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0474

Gnomad OTH AF: 0.0365

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

GnomAD4 genome AF: 0.0366 AC: 5565 AN: 152184 Hom.: 162 Cov.: 32 AF XY: 0.0372 AC XY: 2765 AN XY: 74386

African (AFR) AF: 0.00816 AC: 339 AN: 41520

American (AMR) AF: 0.0361 AC: 552 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.118 AC: 567 AN: 4818

European-Finnish (FIN) AF: 0.0431 AC: 457 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3227 AN: 68008

Other (OTH) AF: 0.0361 AC: 76 AN: 2104

Alfa AF: 0.0392 Hom.: 23

Bravo AF: 0.0323

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs11699311; hg19: chr20-52355331;