rs1482930

Variant names:

• chr15-81571622-A-G
• rs1482930
• ENST00000558141.5:n.28+17592A>G

Variant summary

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

The ENST00000558141.5(TMC3-AS1):​n.28+17592A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,002 control chromosomes in the GnomAD database, including 15,850 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 0.40 (15850 hom., cov: 32)
• Consequence: TMC3-AS1 ENST00000558141.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 3 publications found

Genes affected

TMC3-AS1 (HGNC:51424): (TMC3 antisense RNA 1)

ENSG00000259543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558141.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMC3-AS1	ENST00000558141.5	TSL:3	n.28+17592A>G		intron	N/A
	ENSG00000259543	ENST00000559211.1	TSL:4	n.99-38387A>G		intron	N/A
	TMC3-AS1	ENST00000829087.1		n.1143-75761A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60655 AN: 151884 Hom.: 15824 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.400 AC: 60752 AN: 152002 Hom.: 15850 Cov.: 32 AF XY: 0.400 AC XY: 29751 AN XY: 74332

African (AFR) AF: 0.716 AC: 29683 AN: 41480

American (AMR) AF: 0.462 AC: 7044 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3336 AN: 5156

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4812

European-Finnish (FIN) AF: 0.189 AC: 2001 AN: 10588

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15532 AN: 67930

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.279 Hom.: 3950

Bravo AF: 0.441

Asia WGS AF: 0.427 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.78
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs1482930; hg19: chr15-81863963;