NM_152701.5:c.*924G>A

Variant names:

• chr7-48646436-G-A
• rs3923511
• NM_152701.5:c.*924G>A

Variant summary

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

The NM_152701.5(ABCA13):​c.*924G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,012 control chromosomes in the GnomAD database, including 35,260 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 0.67 (35260 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ABCA13 NM_152701.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA13	NM_152701.5	c.*924G>A		3_prime_UTR_variant	Exon 62 of 62	ENST00000435803.6	NP_689914.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA13	ENST00000435803.6	c.*924G>A		3_prime_UTR_variant	Exon 62 of 62	1	NM_152701.5	ENSP00000411096.1
ABCA13	ENST00000411975.5	c.*924G>A		3_prime_UTR_variant	Exon 19 of 19	2		ENSP00000391042.1
ABCA13	ENST00000544596.5	c.*924G>A		downstream_gene_variant		1		ENSP00000442634.2

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101933 AN: 151894 Hom.: 35236 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.698

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.671 AC: 101993 AN: 152012 Hom.: 35260 Cov.: 32 AF XY: 0.663 AC XY: 49270 AN XY: 74300

African (AFR) AF: 0.509 AC: 21073 AN: 41414

American (AMR) AF: 0.618 AC: 9435 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3430 AN: 5168

South Asian (SAS) AF: 0.699 AC: 3368 AN: 4820

European-Finnish (FIN) AF: 0.679 AC: 7174 AN: 10566

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.772 AC: 52492 AN: 67988

Other (OTH) AF: 0.704 AC: 1483 AN: 2108

Alfa AF: 0.731 Hom.: 130824

Bravo AF: 0.655

Asia WGS AF: 0.682 AC: 2370 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	0.69
DANN	Benign	0.66
PhyloP100		-0.14
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: rs3923511; hg19: chr7-48686032;