13-44211962-C-T

Position:

• chr13-44211962-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.412-26866C>T 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 0.557 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 ENST00000618753.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMIM2-AS1	ENST00000618753.4	n.412-26866C>T		intron_variant, non_coding_transcript_variant		4
SMIM2-AS1	ENST00000437867.6	n.1492-26866C>T		intron_variant, non_coding_transcript_variant		5
SMIM2-AS1	ENST00000659169.2	n.613-26866C>T		intron_variant, non_coding_transcript_variant
SMIM2-AS1	ENST00000666499.1	n.707-26866C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.588

Alfa AF: 0.616 Hom.: 5176

Bravo AF: 0.540

Asia WGS AF: 0.628 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4942296; hg19: chr13-44786098;