2-215011647-T-A

Variant names:

• chr2-215011647-T-A
• rs10198064
• NM_173076.3:c.2124A>T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_173076.3(ABCA12):​c.2124A>T​(p.Ala708Ala) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A708A) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ABCA12 NM_173076.3 splice_region, synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716

Genes affected

ABCA12 (HGNC:14637): (ATP binding cassette subfamily A member 12) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily, which is the only major ABC subfamily found exclusively in multicellular eukaryotes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ENSG00000227769 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP7: Synonymous conserved (PhyloP=-0.716 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA12	NM_173076.3	c.2124A>T	p.Ala708Ala	splice_region_variant, synonymous_variant	Exon 17 of 53	ENST00000272895.12	NP_775099.2
ABCA12	NM_015657.4	c.1170A>T	p.Ala390Ala	splice_region_variant, synonymous_variant	Exon 9 of 45		NP_056472.2
ABCA12	XM_011510951.3	c.2124A>T	p.Ala708Ala	splice_region_variant, synonymous_variant	Exon 17 of 53		XP_011509253.1
ABCA12	NR_103740.2	n.2566A>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 18 of 55

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA12	ENST00000272895.12	c.2124A>T	p.Ala708Ala	splice_region_variant, synonymous_variant	Exon 17 of 53	1	NM_173076.3	ENSP00000272895.7
ABCA12	ENST00000389661.4	c.1170A>T	p.Ala390Ala	splice_region_variant, synonymous_variant	Exon 9 of 45	1		ENSP00000374312.4
ENSG00000227769	ENST00000617699.1	n.29-1409T>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.24
DANN	Benign	0.53

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: rs10198064; hg19: chr2-215876371;