rs1415639

Variant names:

• chr13-44705575-G-A
• rs1415639
• ENST00000611081.1:n.93+9726C>T

Variant summary

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

The ENST00000611081.1(ENSG00000276527):​n.93+9726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,058 control chromosomes in the GnomAD database, including 2,174 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 0.12 (2174 hom., cov: 32)
• Consequence: ENSG00000276527 ENST00000611081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 1 publications found

Genes affected

ENSG00000276527 (HGNC:):

TSC22D1-AS1 (HGNC:43684): (TSC22D1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611081.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000276527	ENST00000611081.1	TSL:3	n.93+9726C>T		intron	N/A
	TSC22D1-AS1	ENST00000715720.1		n.546-7672G>A		intron	N/A
	TSC22D1-AS1	ENST00000762093.1		n.515-10140G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18527 AN: 151940 Hom.: 2167 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.122 AC: 18566 AN: 152058 Hom.: 2174 Cov.: 32 AF XY: 0.119 AC XY: 8850 AN XY: 74370

African (AFR) AF: 0.309 AC: 12828 AN: 41448

American (AMR) AF: 0.0635 AC: 969 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3470

East Asian (EAS) AF: 0.0493 AC: 255 AN: 5174

South Asian (SAS) AF: 0.0926 AC: 446 AN: 4816

European-Finnish (FIN) AF: 0.0451 AC: 477 AN: 10584

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0453 AC: 3081 AN: 67974

Other (OTH) AF: 0.0940 AC: 199 AN: 2116

Alfa AF: 0.0916 Hom.: 532

Bravo AF: 0.131

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.14
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1415639; hg19: chr13-45279711;