13-44211962-C-T

Variant names:

• chr13-44211962-C-T
• rs4942296
• ENST00000437867.6:n.1492-26866C>T

Variant summary

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

The ENST00000437867.6(SMIM2-AS1):​n.1492-26866C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,120 control chromosomes in the GnomAD database, including 26,515 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 0.56 (26515 hom., cov: 33)
• Consequence: SMIM2-AS1 ENST00000437867.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM2-AS1	ENST00000437867.6	TSL:5	n.1492-26866C>T		intron	N/A
	SMIM2-AS1	ENST00000618753.4	TSL:4	n.412-26866C>T		intron	N/A
	SMIM2-AS1	ENST00000659169.2		n.613-26866C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84749 AN: 152002 Hom.: 26489 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.557 AC: 84776 AN: 152120 Hom.: 26515 Cov.: 33 AF XY: 0.564 AC XY: 41967 AN XY: 74370

African (AFR) AF: 0.239 AC: 9930 AN: 41486

American (AMR) AF: 0.677 AC: 10346 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3472

East Asian (EAS) AF: 0.643 AC: 3322 AN: 5166

South Asian (SAS) AF: 0.662 AC: 3195 AN: 4828

European-Finnish (FIN) AF: 0.724 AC: 7665 AN: 10592

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46079 AN: 67980

Other (OTH) AF: 0.588 AC: 1242 AN: 2114

Alfa AF: 0.605 Hom.: 5206

Bravo AF: 0.540

Asia WGS AF: 0.628 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.3
DANN	Benign	0.87
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs4942296; hg19: chr13-44786098;