10-1033639-C-T

Variant names:

• chr10-1033639-C-T
• rs3793779
• ENST00000420381.5:n.117-1651C>T

Variant summary

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

The ENST00000420381.5(IDI2-AS1):​n.117-1651C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,964 control chromosomes in the GnomAD database, including 8,842 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 0.34 (8842 hom., cov: 32)
• Consequence: IDI2-AS1 ENST00000420381.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 3 publications found

Genes affected

IDI2-AS1 (HGNC:30885): (IDI2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IDI2-AS1	NR_024628.1	n.148-2175C>T		intron_variant	Intron 1 of 3
IDI2-AS1	NR_024629.1	n.148-3150C>T		intron_variant	Intron 1 of 2
IDI2-AS1	NR_027708.1	n.148-1651C>T		intron_variant	Intron 1 of 4
IDI2-AS1	NR_027709.1	n.148-1651C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IDI2-AS1	ENST00000420381.5	n.117-1651C>T		intron_variant	Intron 1 of 4	1
IDI2-AS1	ENST00000428780.5	n.207-2175C>T		intron_variant	Intron 1 of 3	1
IDI2-AS1	ENST00000437374.6	n.119-2175C>T		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51277 AN: 151846 Hom.: 8834 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.338 AC: 51313 AN: 151964 Hom.: 8842 Cov.: 32 AF XY: 0.338 AC XY: 25115 AN XY: 74252

African (AFR) AF: 0.291 AC: 12066 AN: 41422

American (AMR) AF: 0.380 AC: 5802 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2137 AN: 5168

South Asian (SAS) AF: 0.352 AC: 1694 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3252 AN: 10526

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23456 AN: 67968

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.336 Hom.: 2288

Bravo AF: 0.344

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs3793779; hg19: chr10-1079579;