13-44111810-A-G

Variant summary

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

The NR_104065.1(SMIM2-AS1):n.64+1198A>G 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 0.661 in 152,074 control chromosomes in the GnomAD database, including 37,312 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 0.66 (37312 hom., cov: 32)
• Consequence: SMIM2-AS1 NR_104065.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

Genes affected

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

LINC00390 (HGNC:42718): (long intergenic non-protein coding RNA 390)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMIM2-AS1	NR_104065.1	n.64+1198A>G		intron_variant, non_coding_transcript_variant
LINC00390	NR_132368.1	n.327-4593T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM2-AS1	ENST00000618753.4	n.162+1198A>G		intron_variant, non_coding_transcript_variant		4
LINC00390	ENST00000662947.1	n.327-14736T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100529 AN: 151956 Hom.: 37314 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.661 AC: 100531 AN: 152074 Hom.: 37312 Cov.: 32 AF XY: 0.663 AC XY: 49242 AN XY: 74320

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.726

Alfa AF: 0.811 Hom.: 83112

Bravo AF: 0.642

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717091; hg19: chr13-44685946;