rs298638

Variant names:

• chr5-61177226-G-T
• rs298638
• ENST00000506902.2:n.458-2478G>T

Variant summary

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

The ENST00000506902.2(SMIM15-AS1):​n.458-2478G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 152,138 control chromosomes in the GnomAD database, including 159 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 0.022 (159 hom., cov: 32)
• Consequence: SMIM15-AS1 ENST00000506902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM15-AS1	NR_109908.1		n.212-2478G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM15-AS1	ENST00000506902.2	TSL:3	n.458-2478G>T		intron	N/A
	SMIM15-AS1	ENST00000821105.1		n.59-2478G>T		intron	N/A
	SMIM15-AS1	ENST00000821106.1		n.154-2478G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3307 AN: 152020 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.00391

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00941

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0217 AC: 3309 AN: 152138 Hom.: 159 Cov.: 32 AF XY: 0.0253 AC XY: 1885 AN XY: 74368

African (AFR) AF: 0.00390 AC: 162 AN: 41520

American (AMR) AF: 0.0371 AC: 567 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5164

South Asian (SAS) AF: 0.0847 AC: 407 AN: 4804

European-Finnish (FIN) AF: 0.0333 AC: 353 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00941 AC: 640 AN: 67982

Other (OTH) AF: 0.0232 AC: 49 AN: 2108

Alfa AF: 0.0121 Hom.: 4

Bravo AF: 0.0220

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.61
DANN	Benign	0.70
PhyloP100		-0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs298638;

hg19: chr5-60473053;