Variant chr19-1854558-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_031918.4(KLF16):c.660T>C(p.Pro220=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,567,310 control chromosomes in the GnomAD database, including 59,909 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 0.36 ( 11920 hom., cov: 33)

Exomes 𝑓: 0.25 ( 47989 hom. )

Consequence

KLF16
NM_031918.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.83

Variant links:

Genes affected

KLF16 (HGNC:16857): (KLF transcription factor 16) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within dopamine receptor signaling pathway. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

KLF16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-3.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF16	NM_031918.4 linkuse as main transcript	c.660T>C	p.Pro220=	synonymous_variant	2/2	ENST00000250916.6	NP_114124.1
KLF16	XM_047439498.1 linkuse as main transcript	c.630T>C	p.Pro210=	synonymous_variant	2/2		XP_047295454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
KLF16	ENST00000250916.6 linkuse as main transcript	c.660T>C	p.Pro220=	synonymous_variant	2/2	1	NM_031918.4	ENSP00000250916	P1
KLF16	ENST00000617223.1 linkuse as main transcript	c.660T>C	p.Pro220=	synonymous_variant	2/3	1		ENSP00000483701	P1
KLF16	ENST00000541015.5 linkuse as main transcript	c.660T>C	p.Pro220=	synonymous_variant, NMD_transcript_variant	2/3	1		ENSP00000439973
KLF16	ENST00000592313.1 linkuse as main transcript	c.249T>C	p.Pro83=	synonymous_variant	2/2	3		ENSP00000480570

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54352

AN:

151654

Hom.:

11898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.609

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.317

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.342

GnomAD3 exomes

AF:

0.298

AC:

54480

AN:

182616

Hom.:

9168

AF XY:

0.287

AC XY:

29073

AN XY:

101126

show subpopulations

Gnomad AFR exome

AF:

0.609

Gnomad AMR exome

AF:

0.407

Gnomad ASJ exome

AF:

0.266

Gnomad EAS exome

AF:

0.388

Gnomad SAS exome

AF:

0.291

Gnomad FIN exome

AF:

0.207

Gnomad NFE exome

AF:

0.223

Gnomad OTH exome

AF:

0.275

GnomAD4 exome

AF:

0.247

AC:

349833

AN:

1415540

Hom.:

47989

Cov.:

AF XY:

0.248

AC XY:

174041

AN XY:

702488

show subpopulations

Gnomad4 AFR exome

AF:

0.635

Gnomad4 AMR exome

AF:

0.408

Gnomad4 ASJ exome

AF:

0.270

Gnomad4 EAS exome

AF:

0.448

Gnomad4 SAS exome

AF:

0.290

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.270

GnomAD4 genome

AF:

0.359

AC:

54417

AN:

151770

Hom.:

11920

Cov.:

AF XY:

0.358

AC XY:

26520

AN XY:

74164

show subpopulations

Gnomad4 AFR

AF:

0.609

Gnomad4 AMR

AF:

0.399

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.413

Gnomad4 SAS

AF:

0.307

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.225

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.286

Hom.:

1399

Bravo

AF:

0.383

Asia WGS

AF:

0.365

AC:

1268

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.18

DANN

Benign

0.40

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over