4-139631245-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_939252.3(QKILA):n.111-2570G>A variant causes a intron, non coding transcript 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 XR_939252.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551

Genes affected

QKILA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QKILA	XR_939252.3	n.111-2570G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.599

Alfa AF: 0.533 Hom.: 44257

Bravo AF: 0.562

Asia WGS AF: 0.537 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1027472; hg19: chr4-140552399;