rs75598935

Variant names:

• chr15-79927251-G-A
• rs75598935
• ENST00000560255.3:n.4481G>A

Variant summary

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

The ENST00000560255.3(ST20-AS1):​n.4481G>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 0.0218 in 152,276 control chromosomes in the GnomAD database, including 78 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 0.022 (78 hom., cov: 31)
• Consequence: ST20-AS1 ENST00000560255.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 2 publications found

Genes affected

ST20-AS1 (HGNC:27521): (ST20 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0218 (3317/152276) while in subpopulation SAS AF = 0.0323 (156/4832). AF 95% confidence interval is 0.0282. There are 78 homozygotes in GnomAd4. There are 1868 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 78 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
ST20-AS1	ENST00000560255.3	n.4481G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3317 AN: 152158 Hom.: 78 Cov.: 31

Gnomad AFR AF: 0.00396

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0218 AC: 3317 AN: 152276 Hom.: 78 Cov.: 31 AF XY: 0.0251 AC XY: 1868 AN XY: 74450

African (AFR) AF: 0.00395 AC: 164 AN: 41568

American (AMR) AF: 0.0107 AC: 163 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4832

European-Finnish (FIN) AF: 0.0985 AC: 1042 AN: 10582

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1733 AN: 68024

Other (OTH) AF: 0.0151 AC: 32 AN: 2116

Alfa AF: 0.0257 Hom.: 12

Bravo AF: 0.0134

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.97
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs75598935; hg19: chr15-80219593;