19-16324634-G-A

Position:

• chr19-16324634-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_186323.1(KLF2-DT):​n.37C>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 0.0392 in 157,568 control chromosomes in the GnomAD database, including 188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.039 (184 hom., cov: 32)
  • Exomes 𝑓: 0.032 (4 hom.)
• Consequence: KLF2-DT NR_186323.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0150

Genes affected

KLF2-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 19-16324634-G-A is Benign according to our data. Variant chr19-16324634-G-A is described in ClinVar as [Benign]. Clinvar id is 1246322.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF2-DT	NR_186323.1	n.37C>T		non_coding_transcript_exon_variant	1/2
		n.16324634G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5969 AN: 151404 Hom.: 184 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0658

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0481

GnomAD4 exome AF: 0.0319 AC: 193 AN: 6054 Hom.: 4 AF XY: 0.0300 AC XY: 96 AN XY: 3198

Gnomad4 AFR exome AF: 0.0991

Gnomad4 AMR exome AF: 0.127

Gnomad4 ASJ exome AF: 0.0798

Gnomad4 EAS exome AF: 0.0357

Gnomad4 SAS exome AF: 0.0156

Gnomad4 FIN exome AF: 0.0272

Gnomad4 NFE exome AF: 0.0225

Gnomad4 OTH exome AF: 0.0353

GnomAD4 genome AF: 0.0395 AC: 5983 AN: 151514 Hom.: 184 Cov.: 32 AF XY: 0.0401 AC XY: 2969 AN XY: 74050

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0658

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0476

Alfa AF: 0.00228 Hom.: 0

Bravo AF: 0.0478

Asia WGS AF: 0.0270 AC: 93 AN: 3412

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745317; hg19: chr19-16435445;