5-61203304-A-G

Variant names:

• chr5-61203304-A-G
• rs171748
• ENST00000506902.2:n.668+22866A>G

Variant summary

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

The ENST00000506902.2(SMIM15-AS1):​n.668+22866A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,998 control chromosomes in the GnomAD database, including 28,435 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 0.60 (28435 hom., cov: 31)
• Consequence: SMIM15-AS1 ENST00000506902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 18 publications found

Genes affected

SMIM15-AS1 (HGNC:41293): (SMIM15 antisense RNA 1)

LINC02057 (HGNC:52900): (long intergenic non-protein coding RNA 2057)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506902.2. 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
	SMIM15-AS1	NR_109908.1		n.422+22866A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM15-AS1	ENST00000506902.2	TSL:3	n.668+22866A>G		intron	N/A
	LINC02057	ENST00000511794.6	TSL:3	n.470-1600T>C		intron	N/A
	LINC02057	ENST00000661728.1		n.551-1600T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91142 AN: 151880 Hom.: 28414 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.600 AC: 91201 AN: 151998 Hom.: 28435 Cov.: 31 AF XY: 0.597 AC XY: 44313 AN XY: 74280

African (AFR) AF: 0.759 AC: 31449 AN: 41454

American (AMR) AF: 0.529 AC: 8082 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1972 AN: 3470

East Asian (EAS) AF: 0.785 AC: 4055 AN: 5166

South Asian (SAS) AF: 0.471 AC: 2264 AN: 4810

European-Finnish (FIN) AF: 0.539 AC: 5680 AN: 10536

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35688 AN: 67978

Other (OTH) AF: 0.600 AC: 1266 AN: 2110

Alfa AF: 0.566 Hom.: 35996

Bravo AF: 0.611

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs171748; hg19: chr5-60499131;