rs12185505

Variant names:

• chr19-16290012-C-A
• rs12185505
• ENST00000588799.2:n.238-6291G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-16290012-C-A
• chr19-16290012-C-G
• chr19-16290012-C-T

Variant summary

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

The ENST00000588799.2(KLF2-DT):​n.238-6291G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,736 control chromosomes in the GnomAD database, including 4,719 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 0.21 (4719 hom., cov: 31)
• Consequence: KLF2-DT ENST00000588799.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF2-DT	NR_186323.1	n.365-6291G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF2-DT	ENST00000588799.2	n.238-6291G>T		intron_variant	Intron 1 of 1	2
KLF2-DT	ENST00000588945.2	n.350+2819G>T		intron_variant	Intron 2 of 2	3
KLF2-DT	ENST00000810104.1	n.140-6291G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32564 AN: 151616 Hom.: 4715 Cov.: 31

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.215 AC: 32572 AN: 151736 Hom.: 4719 Cov.: 31 AF XY: 0.219 AC XY: 16217 AN XY: 74168

African (AFR) AF: 0.0560 AC: 2318 AN: 41378

American (AMR) AF: 0.219 AC: 3342 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3436 AN: 5152

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2613 AN: 10510

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17624 AN: 67870

Other (OTH) AF: 0.227 AC: 479 AN: 2108

Alfa AF: 0.220 Hom.: 1935

Bravo AF: 0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.83
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12185505; hg19: chr19-16400823;