rs1044994

Variant names:

• chr12-110038790-T-A
• rs1044994
• NM_033121.2:c.*1236T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-110038790-T-A
• chr12-110038790-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

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

Our verdict: Benign. The variant received -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.

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.*1236T>A		3_prime_UTR	Exon 15 of 15	NP_149112.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13A	ENST00000261739.9	TSL:1 MANE Select	c.*1236T>A		3_prime_UTR	Exon 15 of 15	ENSP00000261739.4
	ANKRD13A	ENST00000553251.5	TSL:2	n.2677T>A		non_coding_transcript_exon	Exon 6 of 6
	C12orf76	ENST00000546651.3	TSL:2	n.193+9573A>T		intron	N/A

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

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) AF: 0.0532 AC: 5 AN: 94

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.464 AC: 19229 AN: 41426

American (AMR) AF: 0.110 AC: 1684 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0445 AC: 154 AN: 3464

East Asian (EAS) AF: 0.132 AC: 683 AN: 5178

South Asian (SAS) AF: 0.148 AC: 713 AN: 4824

European-Finnish (FIN) AF: 0.0608 AC: 645 AN: 10612

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4992 AN: 67998

Other (OTH) AF: 0.149 AC: 314 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.88
PhyloP100		1.6
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: rs1044994; hg19: chr12-110476595;