rs4885162

Variant names:

• chr13-74295211-T-C
• rs4885162
• NM_001400139.1:c.-32+10785A>G

Variant summary

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

The NM_001400139.1(KLF12):​c.-32+10785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,006 control chromosomes in the GnomAD database, including 27,213 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 0.54 (27213 hom., cov: 31)
• Consequence: KLF12 NM_001400139.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 3 publications found

Genes affected

KLF12 (HGNC:6346): (KLF transcription factor 12) Activator protein-2 alpha (AP-2 alpha) is a developmentally-regulated transcription factor and important regulator of gene expression during vertebrate development and carcinogenesis. The protein encoded by this gene is a member of the Kruppel-like zinc finger protein family and can repress expression of the AP-2 alpha gene by binding to a specific site in the AP-2 alpha gene promoter. Repression by the encoded protein requires binding with a corepressor, CtBP1. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

LINC00402 (HGNC:42732): (long intergenic non-protein coding RNA 402)

ENSG00000289644 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001400139.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF12	NM_001400139.1		c.-32+10785A>G		intron	N/A	NP_001387068.1	Q9Y4X4-1
	KLF12	NM_001400153.1		c.-32+10785A>G		intron	N/A	NP_001387082.1	Q9Y4X4-3
	LOC105370259	NR_187793.1		n.150+6992T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00402	ENST00000653841.1		n.148+6992T>C		intron	N/A
	LINC00402	ENST00000653992.1		n.150+6992T>C		intron	N/A
	LINC00402	ENST00000654479.1		n.129+6992T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81835 AN: 151886 Hom.: 27208 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.538 AC: 81846 AN: 152006 Hom.: 27213 Cov.: 31 AF XY: 0.535 AC XY: 39770 AN XY: 74302

African (AFR) AF: 0.138 AC: 5722 AN: 41484

American (AMR) AF: 0.632 AC: 9655 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2061 AN: 3466

East Asian (EAS) AF: 0.523 AC: 2702 AN: 5164

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4826

European-Finnish (FIN) AF: 0.690 AC: 7272 AN: 10540

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50350 AN: 67932

Other (OTH) AF: 0.553 AC: 1168 AN: 2112

Alfa AF: 0.603 Hom.: 27155

Bravo AF: 0.525

Asia WGS AF: 0.434 AC: 1506 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.56
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4885162; hg19: chr13-74869348;