rs7295290

chr12-110016585-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033121.2(ANKRD13A):c.400+152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 670,132 control chromosomes in the GnomAD database, including 2,276 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 0.082 (550 hom., cov: 32)
  • Exomes 𝑓: 0.071 (1726 hom.)
• Consequence: ANKRD13A NM_033121.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

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

Verdict is Benign. Variant got -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 = 0.0922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD13A	NM_033121.2	c.400+152C>T		intron_variant		ENST00000261739.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD13A	ENST00000261739.9	c.400+152C>T		intron_variant		1	NM_033121.2	P1
ANKRD13A	ENST00000553025.5	c.136+152C>T		intron_variant, NMD_transcript_variant		1
ANKRD13A	ENST00000550404.1	n.659+152C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12490 AN: 151970 Hom.: 549 Cov.: 32

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.100

GnomAD4 exome AF: 0.0715 AC: 37018 AN: 518044 Hom.: 1726 AF XY: 0.0723 AC XY: 19122 AN XY: 264360

Gnomad4 AFR exome AF: 0.0936

Gnomad4 AMR exome AF: 0.0558

Gnomad4 ASJ exome AF: 0.143

Gnomad4 EAS exome AF: 0.000232

Gnomad4 SAS exome AF: 0.0717

Gnomad4 FIN exome AF: 0.0593

Gnomad4 NFE exome AF: 0.0751

Gnomad4 OTH exome AF: 0.0788

GnomAD4 genome AF: 0.0822 AC: 12500 AN: 152088 Hom.: 550 Cov.: 32 AF XY: 0.0814 AC XY: 6053 AN XY: 74322

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0830

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0839 Hom.: 102

Bravo AF: 0.0828

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.5
Dann	Benign	0.76

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: rs7295290; hg19: chr12-110454390;