2-172550832-C-T

Variant names:

• chr2-172550832-C-T
• rs12151618
• ENST00000442417.5:n.441+5257G>A

Variant summary

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

The ENST00000442417.5(ITGA6-AS1):​n.441+5257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,956 control chromosomes in the GnomAD database, including 12,055 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 0.36 (12055 hom., cov: 32)
• Consequence: ITGA6-AS1 ENST00000442417.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 9 publications found

Genes affected

ITGA6-AS1 (HGNC:40308): (ITGA6 antisense RNA 1)

PDK1-AS1 (HGNC:40441): (PDK1 and ITGA6 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDK1-AS1	NR_186177.1	n.376+5257G>A		intron_variant	Intron 1 of 3
PDK1-AS1	NR_186178.1	n.376+5257G>A		intron_variant	Intron 1 of 2
PDK1-AS1	NR_199651.1	n.376+5257G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA6-AS1	ENST00000442417.5	n.441+5257G>A		intron_variant	Intron 1 of 3	3
ITGA6-AS1	ENST00000450443.1	n.508+5257G>A		intron_variant	Intron 1 of 2	3
ITGA6-AS1	ENST00000715602.2	n.205+1773G>A		intron_variant	Intron 1 of 3
ITGA6-AS1	ENST00000830319.1	n.93+4997G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53905 AN: 151838 Hom.: 12003 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.356 AC: 54029 AN: 151956 Hom.: 12055 Cov.: 32 AF XY: 0.354 AC XY: 26307 AN XY: 74268

African (AFR) AF: 0.635 AC: 26293 AN: 41436

American (AMR) AF: 0.341 AC: 5202 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1657 AN: 5152

South Asian (SAS) AF: 0.362 AC: 1740 AN: 4806

European-Finnish (FIN) AF: 0.198 AC: 2093 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15158 AN: 67960

Other (OTH) AF: 0.315 AC: 665 AN: 2112

Alfa AF: 0.277 Hom.: 14143

Bravo AF: 0.380

Asia WGS AF: 0.378 AC: 1311 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	4.0
DANN	Benign	0.49
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs12151618; hg19: chr2-173415560;