rs41305896

Variant names:

• chr5-52979888-T-C
• rs41305896
• ENST00000503559.1:n.263-1489A>G

Variant summary

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

The ENST00000503559.1(ITGA2-AS1):​n.263-1489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 152,318 control chromosomes in the GnomAD database, including 87 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 0.031 (87 hom., cov: 33)
• Consequence: ITGA2-AS1 ENST00000503559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 3 publications found

Genes affected

ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0308 (4697/152318) while in subpopulation NFE AF = 0.0341 (2316/68016). AF 95% confidence interval is 0.0329. There are 87 homozygotes in GnomAd4. There are 2359 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 87 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA2-AS1	NR_186583.1	n.270+8316A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA2-AS1	ENST00000503559.1	n.263-1489A>G		intron_variant	Intron 2 of 4	5
ITGA2-AS1	ENST00000505701.5	n.263-1489A>G		intron_variant	Intron 2 of 4	4
ITGA2-AS1	ENST00000662246.1	n.148+8316A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0308 AC: 4686 AN: 152200 Hom.: 87 Cov.: 33

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0308 AC: 4697 AN: 152318 Hom.: 87 Cov.: 33 AF XY: 0.0317 AC XY: 2359 AN XY: 74482

African (AFR) AF: 0.0281 AC: 1167 AN: 41570

American (AMR) AF: 0.0206 AC: 315 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 205 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4822

European-Finnish (FIN) AF: 0.0471 AC: 500 AN: 10618

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2316 AN: 68016

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0422 Hom.: 24

Bravo AF: 0.0279

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.58
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs41305896; hg19: chr5-52275718;