rs9533799

Variant names:

• chr13-44234038-C-A
• rs9533799
• ENST00000437867.6:n.1492-4790C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-44234038-C-A
• chr13-44234038-C-G
• chr13-44234038-C-T

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 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

Genes affected

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

LINC02938 (HGNC:55952): (long intergenic non-protein coding RNA 2938)

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM2-AS1	ENST00000437867.6	n.1492-4790C>A		intron_variant	Intron 2 of 2	5
SMIM2-AS1	ENST00000618753.4	n.412-4790C>A		intron_variant	Intron 3 of 3	4
SMIM2-AS1	ENST00000659169.2	n.613-4790C>A		intron_variant	Intron 3 of 3

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;