2-214932094-A-AC

Variant names:

• chr2-214932094-A-AC
• rs139753893
• NM_173076.3:c.*539dupG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_173076.3(ABCA12):​c.*539dupG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 164,732 control chromosomes in the GnomAD database, including 1,321 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.072 (1319 hom., cov: 31)
  • Exomes 𝑓: 0.0038 (2 hom.)
• Consequence: ABCA12 NM_173076.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.601
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 2-214932094-A-AC is Benign according to our data. Variant chr2-214932094-A-AC is described in ClinVar as Likely_benign. ClinVar VariationId is 334212.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173076.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA12	NM_173076.3	MANE Select	c.*539dupG		3_prime_UTR	Exon 53 of 53	NP_775099.2
	ABCA12	NM_015657.4		c.*539dupG		3_prime_UTR	Exon 45 of 45	NP_056472.2
	ABCA12	NR_103740.2		n.8825dupG		non_coding_transcript_exon	Exon 55 of 55

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA12	ENST00000272895.12	TSL:1 MANE Select	c.*539dupG		3_prime_UTR	Exon 53 of 53	ENSP00000272895.7	Q86UK0-1
	SNHG31	ENST00000607412.2	TSL:2	n.351-15730dupC		intron	N/A
	SNHG31	ENST00000655899.1		n.370-28298dupC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10891 AN: 152084 Hom.: 1315 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00112

Gnomad OTH AF: 0.0589

GnomAD4 exome AF: 0.00375 AC: 47 AN: 12530 Hom.: 2 Cov.: 0 AF XY: 0.00410 AC XY: 27 AN XY: 6580

African (AFR) AF: 0.140 AC: 7 AN: 50

American (AMR) AF: 0.0139 AC: 25 AN: 1794

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 132

East Asian (EAS) AF: 0.00 AC: 0 AN: 480

South Asian (SAS) AF: 0.00169 AC: 2 AN: 1186

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 336

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 30

European-Non Finnish (NFE) AF: 0.000879 AC: 7 AN: 7960

Other (OTH) AF: 0.0107 AC: 6 AN: 562

GnomAD4 genome AF: 0.0717 AC: 10915 AN: 152202 Hom.: 1319 Cov.: 31 AF XY: 0.0693 AC XY: 5156 AN XY: 74426

African (AFR) AF: 0.248 AC: 10270 AN: 41462

American (AMR) AF: 0.0283 AC: 433 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00110 AC: 75 AN: 68032

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0826

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Congenital ichthyosiform erythroderma (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs139753893; hg19: chr2-215796818;