17-29595257-A-G

Variant names:

• chr17-29595257-A-G
• rs3110492
• NM_152345.5:c.114+1522A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152345.5(ANKRD13B):​c.114+1522A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,142 control chromosomes in the GnomAD database, including 29,491 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 0.62 (29491 hom., cov: 32)
• Consequence: ANKRD13B NM_152345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 12 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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152345.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13B	NM_152345.5	MANE Select	c.114+1522A>G		intron	N/A	NP_689558.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13B	ENST00000394859.8	TSL:2 MANE Select	c.114+1522A>G		intron	N/A	ENSP00000378328.3	Q86YJ7-1
	ANKRD13B	ENST00000487527.5	TSL:1	n.80+5395A>G		intron	N/A
	ANKRD13B	ENST00000930025.1		c.114+1522A>G		intron	N/A	ENSP00000600084.1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94405 AN: 152024 Hom.: 29456 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.621 AC: 94486 AN: 152142 Hom.: 29491 Cov.: 32 AF XY: 0.621 AC XY: 46187 AN XY: 74380

African (AFR) AF: 0.634 AC: 26330 AN: 41504

American (AMR) AF: 0.615 AC: 9390 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3920 AN: 5170

South Asian (SAS) AF: 0.612 AC: 2949 AN: 4820

European-Finnish (FIN) AF: 0.548 AC: 5811 AN: 10598

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41893 AN: 67982

Other (OTH) AF: 0.620 AC: 1310 AN: 2114

Alfa AF: 0.614 Hom.: 51035

Bravo AF: 0.624

Asia WGS AF: 0.670 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.69
PhyloP100		-0.049
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: rs3110492; hg19: chr17-27922275;