rs956133

chr2-214958622-A-G

Variant summary

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

The NM_173076.3(ABCA12):c.5940-168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,042 control chromosomes in the GnomAD database, including 23,566 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 0.55 (23566 hom., cov: 32)
• Consequence: ABCA12 NM_173076.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

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]

SNHG31 (HGNC:54196): (small nucleolar RNA host gene 31)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA12	NM_173076.3	c.5940-168T>C		intron_variant		ENST00000272895.12
SNHG31	NR_110292.1	n.445-3188A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA12	ENST00000272895.12	c.5940-168T>C		intron_variant		1	NM_173076.3	P1
SNHG31	ENST00000670391.1	n.438-3188A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82826 AN: 151926 Hom.: 23530 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.545 AC: 82919 AN: 152042 Hom.: 23566 Cov.: 32 AF XY: 0.546 AC XY: 40609 AN XY: 74328

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.530

Alfa AF: 0.501 Hom.: 9154

Bravo AF: 0.551

Asia WGS AF: 0.454 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.55

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: rs956133; hg19: chr2-215823346;