NM_152345.5:c.114+3426T>C

Variant names:

• chr17-29597161-T-C
• rs3098945
• NM_152345.5:c.114+3426T>C

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+3426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,170 control chromosomes in the GnomAD database, including 6,176 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 0.25 (6176 hom., cov: 33)
• Consequence: ANKRD13B NM_152345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13B	NM_152345.5	MANE Select	c.114+3426T>C		intron	N/A	NP_689558.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13B	ENST00000394859.8	TSL:2 MANE Select	c.114+3426T>C		intron	N/A	ENSP00000378328.3
	ANKRD13B	ENST00000487527.5	TSL:1	n.80+7299T>C		intron	N/A
	ANKRD13B	ENST00000614878.4	TSL:5	c.114+3426T>C		intron	N/A	ENSP00000481530.1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38216 AN: 152052 Hom.: 6143 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.252 AC: 38303 AN: 152170 Hom.: 6176 Cov.: 33 AF XY: 0.246 AC XY: 18293 AN XY: 74408

African (AFR) AF: 0.458 AC: 18996 AN: 41504

American (AMR) AF: 0.205 AC: 3125 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3472

East Asian (EAS) AF: 0.101 AC: 525 AN: 5180

South Asian (SAS) AF: 0.146 AC: 707 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1443 AN: 10618

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

European-Non Finnish (NFE) AF: 0.184 AC: 12504 AN: 67992

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.203 Hom.: 9807

Bravo AF: 0.264

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.43
PhyloP100		0.0080
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: rs3098945; hg19: chr17-27924179;