chr13-44234038-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000437867.6(SMIM2-AS1):​n.1492-4790C>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 ENST00000437867.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 7 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437867.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM2-AS1	ENST00000437867.6	TSL:5	n.1492-4790C>A		intron	N/A
	SMIM2-AS1	ENST00000618753.4	TSL:4	n.412-4790C>A		intron	N/A
	SMIM2-AS1	ENST00000659169.2		n.613-4790C>A		intron	N/A

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

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.316 AC: 13122 AN: 41478

American (AMR) AF: 0.278 AC: 4246 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3468

East Asian (EAS) AF: 0.0942 AC: 488 AN: 5182

South Asian (SAS) AF: 0.357 AC: 1719 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3906 AN: 10564

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24872 AN: 67974

Other (OTH) AF: 0.347 AC: 733 AN: 2112

Alfa AF: 0.358 Hom.: 33602

Bravo AF: 0.326

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9533799; hg19: chr13-44808174;