rs2864527

Variant names:

• chr18-9288458-T-G
• rs2864527
• ENST00000822310.1:n.513-214A>C

Variant summary

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

The ENST00000822310.1(TWSG1-DT):​n.513-214A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0348 in 152,320 control chromosomes in the GnomAD database, including 116 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 0.035 (116 hom., cov: 33)
• Consequence: TWSG1-DT ENST00000822310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849
• Publications: 4 publications found

Genes affected

TWSG1-DT (HGNC:55329): (TWSG1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0348 (5308/152320) while in subpopulation NFE AF = 0.0411 (2795/68032). AF 95% confidence interval is 0.0398. There are 116 homozygotes in GnomAd4. There are 2452 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 116 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
TWSG1-DT	ENST00000822310.1	n.513-214A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0348 AC: 5296 AN: 152202 Hom.: 115 Cov.: 33

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0173

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0348 AC: 5308 AN: 152320 Hom.: 116 Cov.: 33 AF XY: 0.0329 AC XY: 2452 AN XY: 74484

African (AFR) AF: 0.0387 AC: 1609 AN: 41560

American (AMR) AF: 0.0205 AC: 314 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5194

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4832

European-Finnish (FIN) AF: 0.0173 AC: 184 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2795 AN: 68032

Other (OTH) AF: 0.0350 AC: 74 AN: 2114

Alfa AF: 0.0387 Hom.: 271

Bravo AF: 0.0351

Asia WGS AF: 0.00866 AC: 30 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	2.9
DANN	Benign	0.73
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs2864527; hg19: chr18-9288456;