rs7976412

chr12-110012882-C-G

Variant summary

Our verdict is Benign. Variant got -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

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 = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD13A	NM_033121.2	c.230-243C>G		intron_variant		ENST00000261739.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD13A	ENST00000261739.9	c.230-243C>G		intron_variant		1	NM_033121.2	P1
ANKRD13A	ENST00000553025.5	c.-35-243C>G		intron_variant, NMD_transcript_variant		1
ANKRD13A	ENST00000550404.1	n.489-243C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.258

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.3
Dann	Benign	0.72

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: rs7976412; hg19: chr12-110450687;