11-68130016-C-T

Variant names:

• chr11-68130016-C-T
• rs7944372
• ENST00000530842.3:n.1558C>T

Variant summary

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

The ENST00000530842.3(CHKA-DT):​n.1558C>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 ENST00000530842.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530842.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHKA-DT	NR_183630.1		n.1000C>T		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHKA-DT	ENST00000530842.3	TSL:2	n.1558C>T		non_coding_transcript_exon	Exon 2 of 3
	CHKA-DT	ENST00000802597.1		n.747C>T		non_coding_transcript_exon	Exon 2 of 3
	CHKA-DT	ENST00000802598.1		n.853C>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86519 AN: 151830 Hom.: 24771 Cov.: 32

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.: 37 Cov.: 0 AF XY: 0.580 AC XY: 94 AN XY: 162

African (AFR) AF: 0.583 AC: 7 AN: 12

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.667 AC: 4 AN: 6

South Asian (SAS) AF: 0.833 AC: 5 AN: 6

European-Finnish (FIN) AF: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.556 AC: 89 AN: 160

Other (OTH) AF: 0.500 AC: 6 AN: 12

GnomAD4 genome AF: 0.570 AC: 86570 AN: 151948 Hom.: 24784 Cov.: 32 AF XY: 0.574 AC XY: 42651 AN XY: 74256

African (AFR) AF: 0.519 AC: 21500 AN: 41444

American (AMR) AF: 0.659 AC: 10045 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2143 AN: 3462

East Asian (EAS) AF: 0.665 AC: 3439 AN: 5168

South Asian (SAS) AF: 0.687 AC: 3310 AN: 4820

European-Finnish (FIN) AF: 0.583 AC: 6140 AN: 10536

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38075 AN: 67954

Other (OTH) AF: 0.591 AC: 1245 AN: 2108

Alfa AF: 0.575 Hom.: 77868

Bravo AF: 0.578

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.85
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs7944372; hg19: chr11-67897483;