17-29590753-A-G

Variant names:

• chr17-29590753-A-G
• rs3110496
• ENST00000487527.5:n.80+891A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000487527.5(ANKRD13B):​n.80+891A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,772 control chromosomes in the GnomAD database, including 32,504 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 0.65 (32504 hom., cov: 30)
• Consequence: ANKRD13B ENST00000487527.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 72 publications found

Genes affected

ANKRD13B (HGNC:26363): (ankyrin repeat domain 13B) Enables ubiquitin-dependent protein binding activity. Involved in negative regulation of receptor internalization. Located in endosome; perinuclear region of cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

GIT1 (HGNC:4272): (GIT ArfGAP 1) Enables gamma-tubulin binding activity. Involved in positive regulation of microtubule nucleation and regulation of cytokinesis. Located in several cellular components, including focal adhesion; microtubule cytoskeleton; and mitochondrion. Implicated in attention deficit hyperactivity disorder. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]

ABHD15-AS1 (HGNC:49685): (ABHD15 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487527.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13B	ENST00000487527.5	TSL:1	n.80+891A>G		intron	N/A
	GIT1	ENST00000583413.4	TSL:4	c.88+3189T>C		intron	N/A	ENSP00000466824.1
	ANKRD13B	ENST00000583728.5	TSL:4	c.-283+891A>G		intron	N/A	ENSP00000467078.1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99038 AN: 151654 Hom.: 32471 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.653 AC: 99110 AN: 151772 Hom.: 32504 Cov.: 30 AF XY: 0.651 AC XY: 48306 AN XY: 74152

African (AFR) AF: 0.620 AC: 25628 AN: 41332

American (AMR) AF: 0.641 AC: 9778 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2464 AN: 3470

East Asian (EAS) AF: 0.759 AC: 3902 AN: 5140

South Asian (SAS) AF: 0.643 AC: 3092 AN: 4810

European-Finnish (FIN) AF: 0.592 AC: 6231 AN: 10524

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45931 AN: 67926

Other (OTH) AF: 0.648 AC: 1364 AN: 2104

Alfa AF: 0.671 Hom.: 105657

Bravo AF: 0.654

Asia WGS AF: 0.684 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.80
PhyloP100		2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3110496; hg19: chr17-27917771;