Genetic Variant CHKA-DT:n.1516C>T (chr11-68130016-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000530842.2(CHKA-DT):n.1516C>T 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 0.57 in 152,158 control chromosomes in the GnomAD database, including 24,821 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 0.57 ( 24784 hom., cov: 32)

Exomes 𝑓: 0.57 ( 37 hom. )

Consequence

CHKA-DT
ENST00000530842.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Variant links:

Genes affected

CHKA-DT (HGNC:55504): (CHKA divergent transcript)

CHKA-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHKA-DT	NR_183630.1 link	n.1000C>T		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHKA-DT	ENST00000530842.2 link	n.1516C>T		non_coding_transcript_exon_variant	Exon 2 of 3	2
CHKA-DT	ENST00000527519.2 link	n.152-163C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.570

AC:

86519

AN:

151830

Hom.:

24771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.658

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.688

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.588

GnomAD4 exome

AF:

0.571

AC:

120

AN:

210

Hom.:

Cov.:

AF XY:

0.580

AC XY:

AN XY:

162

show subpopulations

Gnomad4 AFR exome

AF:

0.583

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.667

Gnomad4 SAS exome

AF:

0.833

Gnomad4 FIN exome

AF:

0.625

Gnomad4 NFE exome

AF:

0.556

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.570

AC:

86570

AN:

151948

Hom.:

24784

Cov.:

AF XY:

0.574

AC XY:

42651

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.519

Gnomad4 AMR

AF:

0.659

Gnomad4 ASJ

AF:

0.619

Gnomad4 EAS

AF:

0.665

Gnomad4 SAS

AF:

0.687

Gnomad4 FIN

AF:

0.583

Gnomad4 NFE

AF:

0.560

Gnomad4 OTH

AF:

0.591

Alfa

AF:

0.577

Hom.:

50826

Bravo

AF:

0.578

Asia WGS

AF:

0.638

AC:

2220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.9

DANN

Benign

0.85

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over