19-16324463-C-T

Variant names:

• chr19-16324463-C-T
• rs12459387
• ENST00000588799.2:n.81G>A

Variant summary

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

The ENST00000588799.2(KLF2-DT):​n.81G>A 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 0.135 in 152,298 control chromosomes in the GnomAD database, including 1,536 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 0.14 (1536 hom., cov: 32)
  • Exomes 𝑓: 0.085 (0 hom.)
• Consequence: KLF2-DT ENST00000588799.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 8 publications found

Genes affected

KLF2-DT (HGNC:55304): (KLF2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF2-DT	NR_186323.1	n.208G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF2-DT	ENST00000588799.2	n.81G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
KLF2-DT	ENST00000810106.1	n.81G>A		non_coding_transcript_exon_variant	Exon 1 of 3
KLF2-DT	ENST00000810107.1	n.29G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20585 AN: 152062 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0847 AC: 10 AN: 118 Hom.: 0 Cov.: 0 AF XY: 0.0745 AC XY: 7 AN XY: 94

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0909 AC: 10 AN: 110

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.135 AC: 20604 AN: 152180 Hom.: 1536 Cov.: 32 AF XY: 0.136 AC XY: 10156 AN XY: 74416

African (AFR) AF: 0.172 AC: 7166 AN: 41546

American (AMR) AF: 0.137 AC: 2089 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 336 AN: 3470

East Asian (EAS) AF: 0.0788 AC: 407 AN: 5166

South Asian (SAS) AF: 0.125 AC: 606 AN: 4832

European-Finnish (FIN) AF: 0.185 AC: 1957 AN: 10594

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7548 AN: 67958

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.0483 Hom.: 61

Bravo AF: 0.136

Asia WGS AF: 0.109 AC: 382 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	9.0
DANN	Uncertain	0.99
PhyloP100		-0.072
PromoterAI		-0.035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12459387; hg19: chr19-16435274;