rs10223929

Positions:

• chr7-48364176-G-A

Variant summary

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

The NM_152701.5(ABCA13):​c.10689-3618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,186 control chromosomes in the GnomAD database, including 428 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 0.063 (428 hom., cov: 32)
• Consequence: ABCA13 NM_152701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.094 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA13	NM_152701.5	c.10689-3618G>A		intron_variant		ENST00000435803.6	NP_689914.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA13	ENST00000435803.6	c.10689-3618G>A		intron_variant		1	NM_152701.5	ENSP00000411096	P1
ABCA13	ENST00000544596.5	c.2608-3618G>A		intron_variant		1		ENSP00000442634
ABCA13	ENST00000611776.4	n.2608-3618G>A		intron_variant, non_coding_transcript_variant		1
ABCA13	ENST00000484268.1	n.1173-3618G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9515 AN: 152068 Hom.: 429 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0625 AC: 9514 AN: 152186 Hom.: 428 Cov.: 32 AF XY: 0.0598 AC XY: 4450 AN XY: 74408

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0819 Hom.: 268

Bravo AF: 0.0644

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.79

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: rs10223929; hg19: chr7-48403773;