chr19-16295223-A-G

Variant names:

• chr19-16295223-A-G
• rs390017
• ENST00000588799.2:n.238-11502T>C

Variant summary

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

The ENST00000588799.2(KLF2-DT):​n.238-11502T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,410 control chromosomes in the GnomAD database, including 31,330 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 0.64 (31330 hom., cov: 29)
• Consequence: KLF2-DT ENST00000588799.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF2-DT	NR_186323.1	n.365-11502T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF2-DT	ENST00000588799.2	n.238-11502T>C		intron_variant	Intron 1 of 1	2
KLF2-DT	ENST00000810104.1	n.140-11502T>C		intron_variant	Intron 1 of 1
KLF2-DT	ENST00000810105.1	n.121-2253T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97214 AN: 151292 Hom.: 31304 Cov.: 29

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.643 AC: 97291 AN: 151410 Hom.: 31330 Cov.: 29 AF XY: 0.644 AC XY: 47598 AN XY: 73918

African (AFR) AF: 0.625 AC: 25785 AN: 41258

American (AMR) AF: 0.598 AC: 9093 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2089 AN: 3462

East Asian (EAS) AF: 0.676 AC: 3455 AN: 5114

South Asian (SAS) AF: 0.699 AC: 3358 AN: 4806

European-Finnish (FIN) AF: 0.705 AC: 7354 AN: 10426

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 43995 AN: 67840

Other (OTH) AF: 0.630 AC: 1326 AN: 2104

Alfa AF: 0.639 Hom.: 141029

Bravo AF: 0.632

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs390017; hg19: chr19-16406034;