4-139638583-C-T

Variant names:

• chr4-139638583-C-T
• rs11944754
• ENST00000730152.1:n.130-9908G>A

Variant summary

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

The ENST00000730152.1(QKILA):​n.130-9908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,834 control chromosomes in the GnomAD database, including 7,900 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 0.32 (7900 hom., cov: 32)
• Consequence: QKILA ENST00000730152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QKILA	ENST00000730152.1		n.130-9908G>A		intron	N/A
	QKILA	ENST00000730153.1		n.233-9908G>A		intron	N/A
	ENSG00000295486	ENST00000730420.1		n.111-7443G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47953 AN: 151726 Hom.: 7885 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.316 AC: 47988 AN: 151834 Hom.: 7900 Cov.: 32 AF XY: 0.317 AC XY: 23550 AN XY: 74174

African (AFR) AF: 0.241 AC: 9952 AN: 41270

American (AMR) AF: 0.446 AC: 6805 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1624 AN: 5176

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3109 AN: 10548

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22194 AN: 67966

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.310 Hom.: 987

Bravo AF: 0.327

Asia WGS AF: 0.317 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.14
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11944754; hg19: chr4-140559737;