13-41141146-T-C

Variant names:

• chr13-41141146-T-C
• rs1572018
• ENST00000615685.4:n.98-5281T>C

Variant summary

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

The ENST00000619407.4(ENSG00000278390):​n.118-5281T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,178 control chromosomes in the GnomAD database, including 36,936 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 0.63 (36936 hom., cov: 32)
• Consequence: ENSG00000278390 ENST00000619407.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613

Genes affected

ENSG00000278390 (HGNC:56824): (KBTBD6 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KBTBD6-DT	NR_120423.1	n.129-5281T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278390	ENST00000615685.4	n.98-5281T>C		intron_variant	Intron 1 of 3	4
ENSG00000278390	ENST00000616251.2	n.105-5281T>C		intron_variant	Intron 1 of 3	3
ENSG00000278390	ENST00000619407.4	n.118-5281T>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95360 AN: 152060 Hom.: 36939 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.627 AC: 95342 AN: 152178 Hom.: 36936 Cov.: 32 AF XY: 0.627 AC XY: 46655 AN XY: 74392

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.695

Alfa AF: 0.766 Hom.: 25799

Bravo AF: 0.608

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572018; hg19: chr13-41715282;