2-202040365-T-A

Variant names:

• chr2-202040365-T-A
• rs7583130
• ENST00000733168.1:n.355-679A>T

Variant summary

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

The ENST00000733168.1(KIAA2012-AS1):​n.355-679A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,756 control chromosomes in the GnomAD database, including 13,762 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 0.42 (13762 hom., cov: 31)
• Consequence: KIAA2012-AS1 ENST00000733168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 2 publications found

Genes affected

KIAA2012-AS1 (HGNC:41164): (KIAA2012 antisense RNA 1)

LOC124906114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906114	XR_007088053.1	n.35-679A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA2012-AS1	ENST00000733168.1	n.355-679A>T		intron_variant	Intron 2 of 2
KIAA2012-AS1	ENST00000733169.1	n.223-679A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63068 AN: 151636 Hom.: 13765 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.416 AC: 63096 AN: 151756 Hom.: 13762 Cov.: 31 AF XY: 0.414 AC XY: 30720 AN XY: 74126

African (AFR) AF: 0.297 AC: 12309 AN: 41392

American (AMR) AF: 0.410 AC: 6246 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1348 AN: 5172

South Asian (SAS) AF: 0.457 AC: 2194 AN: 4800

European-Finnish (FIN) AF: 0.502 AC: 5255 AN: 10476

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.490 AC: 33307 AN: 67914

Other (OTH) AF: 0.395 AC: 831 AN: 2106

Alfa AF: 0.452 Hom.: 1986

Bravo AF: 0.404

Asia WGS AF: 0.417 AC: 1447 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7583130; hg19: chr2-202905088;