chr13-44224061-C-T

Position:

• chr13-44224061-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.412-14767C>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 0.296 in 152,054 control chromosomes in the GnomAD database, including 7,198 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 0.30 (7198 hom., cov: 32)
• Consequence: SMIM2-AS1 ENST00000618753.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM2-AS1	ENST00000618753.4	n.412-14767C>T		intron_variant, non_coding_transcript_variant		4
SMIM2-AS1	ENST00000437867.6	n.1492-14767C>T		intron_variant, non_coding_transcript_variant		5
SMIM2-AS1	ENST00000659169.2	n.613-14767C>T		intron_variant, non_coding_transcript_variant
SMIM2-AS1	ENST00000666499.1	n.707-14767C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44995 AN: 151936 Hom.: 7190 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.296 AC: 45024 AN: 152054 Hom.: 7198 Cov.: 32 AF XY: 0.296 AC XY: 21965 AN XY: 74328

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.305

Alfa AF: 0.344 Hom.: 18931

Bravo AF: 0.290

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248414; hg19: chr13-44798197;