12-110012882-C-G

Variant names:

• chr12-110012882-C-G
• rs7976412
• NM_033121.2:c.230-243C>G

Variant summary

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

The NM_033121.2(ANKRD13A):​c.230-243C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,954 control chromosomes in the GnomAD database, including 9,302 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 0.28 (9302 hom., cov: 32)
• Consequence: ANKRD13A NM_033121.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 8 publications found

Genes affected

ANKRD13A (HGNC:21268): (ankyrin repeat domain 13A) Enables ubiquitin-dependent protein binding activity. Involved in negative regulation of protein localization to endosome and negative regulation of receptor internalization. Located in late endosome; perinuclear region of cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033121.2. 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
	ANKRD13A	NM_033121.2	MANE Select	c.230-243C>G		intron	N/A	NP_149112.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13A	ENST00000261739.9	TSL:1 MANE Select	c.230-243C>G		intron	N/A	ENSP00000261739.4
	ANKRD13A	ENST00000550404.1	TSL:1	n.489-243C>G		intron	N/A
	ANKRD13A	ENST00000553025.5	TSL:1	n.-35-243C>G		intron	N/A	ENSP00000474172.1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43142 AN: 151836 Hom.: 9266 Cov.: 32

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.285 AC: 43233 AN: 151954 Hom.: 9302 Cov.: 32 AF XY: 0.281 AC XY: 20873 AN XY: 74296

African (AFR) AF: 0.610 AC: 25282 AN: 41414

American (AMR) AF: 0.186 AC: 2838 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.134 AC: 693 AN: 5154

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4808

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10566

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10580 AN: 67964

Other (OTH) AF: 0.258 AC: 545 AN: 2112

Alfa AF: 0.225 Hom.: 717

Bravo AF: 0.302

Asia WGS AF: 0.228 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		-0.14
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: rs7976412; hg19: chr12-110450687;