chr19-16324200-G-A

Variant names:

• chr19-16324200-G-A
• rs10424657
• ENST00000810114.1:n.362C>T

Variant summary

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

The ENST00000810114.1(KLF2-DT):​n.362C>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 0.261 in 151,952 control chromosomes in the GnomAD database, including 5,759 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 0.26 (5754 hom., cov: 31)
  • Exomes 𝑓: 0.24 (5 hom.)
• Consequence: KLF2-DT ENST00000810114.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810114.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF2-DT	NR_186323.1		n.364+107C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF2-DT	ENST00000810114.1		n.362C>T		non_coding_transcript_exon	Exon 1 of 1
	KLF2-DT	ENST00000588799.2	TSL:2	n.237+107C>T		intron	N/A
	KLF2-DT	ENST00000810104.1		n.139+684C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39600 AN: 151582 Hom.: 5751 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.242 AC: 60 AN: 248 Hom.: 5 AF XY: 0.245 AC XY: 45 AN XY: 184

African (AFR) AF: 0.250 AC: 1 AN: 4

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

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.231 AC: 6 AN: 26

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.245 AC: 46 AN: 188

Other (OTH) AF: 0.250 AC: 4 AN: 16

GnomAD4 genome AF: 0.261 AC: 39620 AN: 151704 Hom.: 5754 Cov.: 31 AF XY: 0.265 AC XY: 19640 AN XY: 74140

African (AFR) AF: 0.129 AC: 5332 AN: 41320

American (AMR) AF: 0.350 AC: 5328 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3462

East Asian (EAS) AF: 0.338 AC: 1740 AN: 5154

South Asian (SAS) AF: 0.394 AC: 1889 AN: 4796

European-Finnish (FIN) AF: 0.270 AC: 2850 AN: 10544

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20663 AN: 67882

Other (OTH) AF: 0.275 AC: 577 AN: 2100

Alfa AF: 0.292 Hom.: 22669

Bravo AF: 0.258

Asia WGS AF: 0.338 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10424657; hg19: chr19-16435011;