13-44234038-C-A

Position:

• chr13-44234038-C-A

Variant summary

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

The ENST00000618753.4(SMIM2-AS1):​n.412-4790C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,092 control chromosomes in the GnomAD database, including 8,684 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 0.33 (8683 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: SMIM2-AS1 ENST00000618753.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

Genes affected

SMIM2-AS1 (HGNC:42674): (SMIM2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM2-AS1	ENST00000618753.4	n.412-4790C>A		intron_variant, non_coding_transcript_variant		4
SMIM2-AS1	ENST00000437867.6	n.1492-4790C>A		intron_variant, non_coding_transcript_variant		5
SMIM2-AS1	ENST00000659169.2	n.613-4790C>A		intron_variant, non_coding_transcript_variant
SMIM2-AS1	ENST00000666499.1	n.707-4790C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50821 AN: 151958 Hom.: 8680 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.250 AC: 4 AN: 16 Hom.: 1 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.334 AC: 50848 AN: 152076 Hom.: 8683 Cov.: 32 AF XY: 0.331 AC XY: 24638 AN XY: 74338

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.0942

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.347

Alfa AF: 0.363 Hom.: 22373

Bravo AF: 0.326

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9533799; hg19: chr13-44808174;