chr7-48431837-C-T

Variant names:

• chr7-48431837-C-T
• rs7357104
• NM_152701.5:c.12565+3966C>T

Variant summary

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

The NM_152701.5(ABCA13):​c.12565+3966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,946 control chromosomes in the GnomAD database, including 6,814 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 0.30 (6814 hom., cov: 32)
• Consequence: ABCA13 NM_152701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152701.5. 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
	ABCA13	NM_152701.5	MANE Select	c.12565+3966C>T		intron	N/A	NP_689914.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA13	ENST00000435803.6	TSL:1 MANE Select	c.12565+3966C>T		intron	N/A	ENSP00000411096.1
	ABCA13	ENST00000544596.5	TSL:1	c.4483+3966C>T		intron	N/A	ENSP00000442634.2
	ABCA13	ENST00000611776.4	TSL:1	n.4484+3966C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45197 AN: 151828 Hom.: 6805 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.298 AC: 45234 AN: 151946 Hom.: 6814 Cov.: 32 AF XY: 0.296 AC XY: 22016 AN XY: 74260

African (AFR) AF: 0.293 AC: 12139 AN: 41446

American (AMR) AF: 0.300 AC: 4573 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1011 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1912 AN: 5160

South Asian (SAS) AF: 0.262 AC: 1264 AN: 4816

European-Finnish (FIN) AF: 0.305 AC: 3205 AN: 10516

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20069 AN: 67964

Other (OTH) AF: 0.295 AC: 623 AN: 2110

Alfa AF: 0.157 Hom.: 297

Bravo AF: 0.297

Asia WGS AF: 0.313 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.45
PhyloP100		-1.1
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: rs7357104; hg19: chr7-48471434;