12-110038790-T-A

Position:

• chr12-110038790-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_033121.2(ANKRD13A):​c.*1236T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,206 control chromosomes in the GnomAD database, including 4,903 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 0.19 (4903 hom., cov: 32)
  • Exomes 𝑓: 0.061 (0 hom.)
• Consequence: ANKRD13A NM_033121.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

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]

C12orf76 (HGNC:33790): (chromosome 12 open reading frame 76) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD13A	NM_033121.2	c.*1236T>A		3_prime_UTR_variant	15/15	ENST00000261739.9	NP_149112.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD13A	ENST00000261739.9	c.*1236T>A		3_prime_UTR_variant	15/15	1	NM_033121.2	ENSP00000261739	P1
ANKRD13A	ENST00000553251.5	n.2677T>A		non_coding_transcript_exon_variant	6/6	2
C12orf76	ENST00000546651.3	n.193+9573A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28422 AN: 151990 Hom.: 4890 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.0612 AC: 6 AN: 98 Hom.: 0 Cov.: 0 AF XY: 0.0172 AC XY: 1 AN XY: 58

Gnomad4 FIN exome AF: 0.0532

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.187 AC: 28486 AN: 152108 Hom.: 4903 Cov.: 32 AF XY: 0.185 AC XY: 13756 AN XY: 74366

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.0734

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0202 Hom.: 15

Bravo AF: 0.202

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.88

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

Other links and lift over

dbSNP: rs1044994; hg19: chr12-110476595;