4-139631245-C-T

Variant names:

• chr4-139631245-C-T
• rs1027472
• ENST00000730152.1:n.130-2570G>A

Variant summary

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

The ENST00000730152.1(QKILA):​n.130-2570G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,972 control chromosomes in the GnomAD database, including 22,952 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 0.55 (22952 hom., cov: 32)
• Consequence: QKILA ENST00000730152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551
• Publications: 7 publications found

Genes affected

QKILA (HGNC:55255): (QKI interacting lncRNA)

ENSG00000295486 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730152.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QKILA	ENST00000730152.1		n.130-2570G>A		intron	N/A
	QKILA	ENST00000730153.1		n.233-2570G>A		intron	N/A
	ENSG00000295486	ENST00000730420.1		n.111-105G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82952 AN: 151854 Hom.: 22919 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.546 AC: 83035 AN: 151972 Hom.: 22952 Cov.: 32 AF XY: 0.550 AC XY: 40834 AN XY: 74270

African (AFR) AF: 0.542 AC: 22434 AN: 41406

American (AMR) AF: 0.690 AC: 10551 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2107 AN: 3466

East Asian (EAS) AF: 0.465 AC: 2402 AN: 5166

South Asian (SAS) AF: 0.547 AC: 2634 AN: 4814

European-Finnish (FIN) AF: 0.542 AC: 5722 AN: 10562

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35187 AN: 67952

Other (OTH) AF: 0.599 AC: 1264 AN: 2110

Alfa AF: 0.533 Hom.: 95331

Bravo AF: 0.562

Asia WGS AF: 0.537 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.49
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1027472; hg19: chr4-140552399;