2-214931578-G-GACAA

Position:

• chr2-214931578-G-GACAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_173076.3(ABCA12):​c.*1055_*1056insTTGT variant causes a 3 prime UTR change. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.33 (9903 hom., cov: 0)
  • Exomes 𝑓: 0.44 (42 hom.)
• Consequence: ABCA12 NM_173076.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.85

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 -10 ACMG points.

• BP6: Variant 2-214931578-G-GACAA is Benign according to our data. Variant chr2-214931578-G-GACAA is described in ClinVar as [Benign]. Clinvar id is 334204.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA12	NM_173076.3	c.*1055_*1056insTTGT		3_prime_UTR_variant	53/53	ENST00000272895.12
SNHG31	NR_110292.1	n.322-16243_322-16240dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA12	ENST00000272895.12	c.*1055_*1056insTTGT		3_prime_UTR_variant	53/53	1	NM_173076.3	P1
SNHG31	ENST00000670391.1	n.438-30228_438-30225dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50714 AN: 151632 Hom.: 9898 Cov.: 0

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.438 AC: 192 AN: 438 Hom.: 42 Cov.: 0 AF XY: 0.455 AC XY: 120 AN XY: 264

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.334 AC: 50727 AN: 151750 Hom.: 9903 Cov.: 0 AF XY: 0.337 AC XY: 24987 AN XY: 74130

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.343

Bravo AF: 0.316

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital ichthyosiform erythroderma Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71399158; hg19: chr2-215796302;