7-48403519-A-G

Variant names:

• chr7-48403519-A-G
• rs10236551
• NM_152701.5:c.11874-164A>G

Variant summary

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

The NM_152701.5(ABCA13):​c.11874-164A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,224 control chromosomes in the GnomAD database, including 3,426 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 0.21 (3426 hom., cov: 33)
• Consequence: ABCA13 NM_152701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 7 publications found

Genes affected

ABCA13 (HGNC:14638): (ATP binding cassette subfamily A member 13) In human, the ATP-binding cassette (ABC) family of transmembrane transporters has at least 48 genes and 7 gene subfamilies. This gene is a member of ABC gene subfamily A (ABCA). Genes within the ABCA family typically encode several thousand amino acids. Like other ABC transmembrane transporter proteins, this protein has 12 or more transmembrane alpha-helix domains that likely arrange to form a single central chamber with multiple substrate binding sites. It is also predicted to have two large extracellular domains and two nucleotide binding domains as is typical for ABCA proteins. Alternative splice variants have been described but their biological validity has not been demonstrated.[provided by RefSeq, Mar 2009]

ABCA13 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA13	NM_152701.5	c.11874-164A>G		intron_variant	Intron 38 of 61	ENST00000435803.6	NP_689914.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA13	ENST00000435803.6	c.11874-164A>G		intron_variant	Intron 38 of 61	1	NM_152701.5	ENSP00000411096.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31482 AN: 152104 Hom.: 3414 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.207 AC: 31529 AN: 152224 Hom.: 3426 Cov.: 33 AF XY: 0.202 AC XY: 15061 AN XY: 74430

African (AFR) AF: 0.191 AC: 7923 AN: 41522

American (AMR) AF: 0.266 AC: 4073 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1107 AN: 5182

South Asian (SAS) AF: 0.133 AC: 642 AN: 4820

European-Finnish (FIN) AF: 0.106 AC: 1126 AN: 10602

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15277 AN: 68010

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.231 Hom.: 6083

Bravo AF: 0.225

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.022
DANN	Benign	0.17
PhyloP100		-2.0
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: rs10236551; hg19: chr7-48443116;