rs10482862

Variant names:

• chr21-14951514-T-C
• rs10482862
• ENST00000432230.6:n.87+62830A>G

Variant summary

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

The ENST00000715910.1(ASMER1):​n.107+91981A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,154 control chromosomes in the GnomAD database, including 1,361 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 0.13 (1361 hom., cov: 32)
• Consequence: ASMER1 ENST00000715910.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 4 publications found

Genes affected

ASMER1 (HGNC:53135): (adipocyte associated metabolic related lncRNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715910.1. 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
	ASMER1	ENST00000432230.6	TSL:5	n.87+62830A>G		intron	N/A
	ASMER1	ENST00000715910.1		n.107+91981A>G		intron	N/A
	ASMER1	ENST00000850670.1		n.114-48518A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19689 AN: 152036 Hom.: 1363 Cov.: 32

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19705 AN: 152154 Hom.: 1361 Cov.: 32 AF XY: 0.132 AC XY: 9832 AN XY: 74390

African (AFR) AF: 0.0796 AC: 3304 AN: 41524

American (AMR) AF: 0.143 AC: 2191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3466

East Asian (EAS) AF: 0.172 AC: 889 AN: 5170

South Asian (SAS) AF: 0.195 AC: 942 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1486 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10174 AN: 67998

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.139 Hom.: 2168

Bravo AF: 0.123

Asia WGS AF: 0.184 AC: 639 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.2
DANN	Benign	0.72
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs10482862; hg19: chr21-16323835;