chr7-48431837-C-T

Position:

• chr7-48431837-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA13	NM_152701.5	c.12565+3966C>T		intron_variant		ENST00000435803.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA13	ENST00000435803.6	c.12565+3966C>T		intron_variant		1	NM_152701.5	P1
ABCA13	ENST00000544596.5	c.4484+3966C>T		intron_variant		1
ABCA13	ENST00000611776.4	n.4484+3966C>T		intron_variant, non_coding_transcript_variant		1
ABCA13	ENST00000453246.5	c.1361+3966C>T		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.295

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.45

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: rs7357104; hg19: chr7-48471434;