rs2318132

Variant names:

• chr20-1823820-C-A
• rs2318132
• ENST00000716594.1:n.951-12596G>T

Variant summary

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

The ENST00000716594.1(ENSG00000286288):​n.951-12596G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,266 control chromosomes in the GnomAD database, including 23 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 0.017 (23 hom., cov: 33)
• Consequence: ENSG00000286288 ENST00000716594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 1 publications found

Genes affected

ENSG00000286288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.017 (2587/152266) while in subpopulation NFE AF = 0.0252 (1717/68022). AF 95% confidence interval is 0.0242. There are 23 homozygotes in GnomAd4. There are 1279 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 23 gene

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
ENSG00000286288	ENST00000716594.1	n.951-12596G>T		intron_variant	Intron 2 of 5
ENSG00000286288	ENST00000844949.1	n.103-44972G>T		intron_variant	Intron 1 of 2
ENSG00000286288	ENST00000844950.1	n.120+37947G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2587 AN: 152148 Hom.: 23 Cov.: 33

Gnomad AFR AF: 0.00512

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0252

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0170 AC: 2587 AN: 152266 Hom.: 23 Cov.: 33 AF XY: 0.0172 AC XY: 1279 AN XY: 74452

African (AFR) AF: 0.00510 AC: 212 AN: 41552

American (AMR) AF: 0.0146 AC: 223 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4832

European-Finnish (FIN) AF: 0.0210 AC: 223 AN: 10608

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0252 AC: 1717 AN: 68022

Other (OTH) AF: 0.0189 AC: 40 AN: 2112

Alfa AF: 0.0206 Hom.: 4

Bravo AF: 0.0173

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2318132; hg19: chr20-1804466;