18-9285826-T-C

Variant names:

• chr18-9285826-T-C
• rs1114591
• NM_015208.5:c.*4700T>C

Variant summary

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

The NM_015208.5(ANKRD12):​c.*4700T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,112 control chromosomes in the GnomAD database, including 4,114 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 (4114 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: ANKRD12 NM_015208.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 7 publications found

Genes affected

ANKRD12 (HGNC:29135): (ankyrin repeat domain 12) This gene encodes a member of the ankyrin repeats-containing cofactor family. These proteins may inhibit the transcriptional activity of nuclear receptors through the recruitment of histone deacetylases. The encoded protein interacts with p160 coactivators and also represses transcription mediated by the coactivator alteration/deficiency in activation 3 (ADA3). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD12	NM_015208.5	c.*4700T>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000262126.9	NP_056023.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD12	ENST00000262126.9	c.*4700T>C		3_prime_UTR_variant	Exon 13 of 13	1	NM_015208.5	ENSP00000262126.3

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31800 AN: 151986 Hom.: 4095 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.209 AC: 31856 AN: 152104 Hom.: 4114 Cov.: 32 AF XY: 0.202 AC XY: 15015 AN XY: 74368

African (AFR) AF: 0.361 AC: 14942 AN: 41444

American (AMR) AF: 0.141 AC: 2151 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3468

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5184

South Asian (SAS) AF: 0.109 AC: 524 AN: 4824

European-Finnish (FIN) AF: 0.0993 AC: 1054 AN: 10610

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11647 AN: 67994

Other (OTH) AF: 0.212 AC: 447 AN: 2110

Alfa AF: 0.183 Hom.: 8305

Bravo AF: 0.219

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1114591; hg19: chr18-9285824;