17-29597161-T-C

Position:

• chr17-29597161-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD13B	NM_152345.5	c.114+3426T>C		intron_variant		ENST00000394859.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD13B	ENST00000394859.8	c.114+3426T>C		intron_variant		2	NM_152345.5	P1
ABHD15-AS1	ENST00000581474.1	n.153+36462T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.220

Alfa AF: 0.179 Hom.: 2824

Bravo AF: 0.264

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.43

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: rs3098945; hg19: chr17-27924179;