XR_005647073.2:n.458T>C

Variant names:

• chr21-37560476-T-C
• rs2835810
• XR_005647073.2:n.458T>C

Variant summary

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

The XR_005647073.2(LOC105372798):​n.458T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 151,850 control chromosomes in the GnomAD database, including 36,116 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 0.69 (36116 hom., cov: 30)
• Consequence: LOC105372798 XR_005647073.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 14 publications found

Genes affected

LOC105372798 (HGNC:):

KCNJ6-AS1 (HGNC:41352): (KCNJ6 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372798	XR_005647073.2	n.458T>C		non_coding_transcript_exon_variant	Exon 1 of 2
KCNJ6-AS1	NR_183540.1	n.407+41434T>C		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104352 AN: 151732 Hom.: 36065 Cov.: 30

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.688 AC: 104468 AN: 151850 Hom.: 36116 Cov.: 30 AF XY: 0.682 AC XY: 50609 AN XY: 74214

African (AFR) AF: 0.727 AC: 30101 AN: 41396

American (AMR) AF: 0.724 AC: 11049 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2501 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3710 AN: 5146

South Asian (SAS) AF: 0.602 AC: 2898 AN: 4810

European-Finnish (FIN) AF: 0.601 AC: 6327 AN: 10534

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45628 AN: 67922

Other (OTH) AF: 0.695 AC: 1461 AN: 2102

Alfa AF: 0.682 Hom.: 162375

Bravo AF: 0.705

Asia WGS AF: 0.699 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.70
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2835810; hg19: chr21-38932778;