rs17712049

chr7-48226598-T-Cchr7-48226598-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152701.5(ABCA13):c.469-664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,232 control chromosomes in the GnomAD database, including 57,823 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 0.87 (57823 hom., cov: 32)
• Consequence: ABCA13 NM_152701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.47

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA13	NM_152701.5	c.469-664T>C		intron_variant		ENST00000435803.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA13	ENST00000435803.6	c.469-664T>C		intron_variant		1	NM_152701.5	P1
ABCA13	ENST00000417403.5	c.469-664T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132388 AN: 152114 Hom.: 57778 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.870 AC: 132489 AN: 152232 Hom.: 57823 Cov.: 32 AF XY: 0.867 AC XY: 64537 AN XY: 74428

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.871

Alfa AF: 0.887 Hom.: 120767

Bravo AF: 0.862

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.11
Dann	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs17712049; hg19: chr7-48266195; COSMIC: COSV70041213;