rs12762955

Variant names:

• chr10-1032842-A-C
• rs12762955
• ENST00000420381.5:n.117-2448A>C

Variant summary

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

The ENST00000420381.5(IDI2-AS1):​n.117-2448A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,938 control chromosomes in the GnomAD database, including 3,328 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 0.20 (3328 hom., cov: 32)
• Consequence: IDI2-AS1 ENST00000420381.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 12 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IDI2-AS1	NR_024628.1	n.148-2972A>C		intron_variant	Intron 1 of 3
IDI2-AS1	NR_024629.1	n.148-3947A>C		intron_variant	Intron 1 of 2
IDI2-AS1	NR_027708.1	n.148-2448A>C		intron_variant	Intron 1 of 4
IDI2-AS1	NR_027709.1	n.148-2448A>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IDI2-AS1	ENST00000420381.5	n.117-2448A>C		intron_variant	Intron 1 of 4	1
IDI2-AS1	ENST00000428780.5	n.207-2972A>C		intron_variant	Intron 1 of 3	1
IDI2-AS1	ENST00000437374.6	n.119-2972A>C		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30857 AN: 151820 Hom.: 3328 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0453

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.203 AC: 30868 AN: 151938 Hom.: 3328 Cov.: 32 AF XY: 0.197 AC XY: 14668 AN XY: 74276

African (AFR) AF: 0.236 AC: 9785 AN: 41444

American (AMR) AF: 0.174 AC: 2659 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3466

East Asian (EAS) AF: 0.0456 AC: 235 AN: 5152

South Asian (SAS) AF: 0.105 AC: 506 AN: 4810

European-Finnish (FIN) AF: 0.179 AC: 1888 AN: 10574

Middle Eastern (MID) AF: 0.157 AC: 45 AN: 286

European-Non Finnish (NFE) AF: 0.215 AC: 14620 AN: 67926

Other (OTH) AF: 0.206 AC: 434 AN: 2102

Alfa AF: 0.209 Hom.: 9633

Bravo AF: 0.206

Asia WGS AF: 0.0870 AC: 305 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	0.88
DANN	Benign	0.45
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12762955; hg19: chr10-1078782;