rs1297214

Variant names:

• chr21-14959532-G-T
• rs1297214
• ENST00000432230.6:n.87+54812C>A

Variant summary

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

The ENST00000715910.1(ASMER1):​n.107+83963C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,074 control chromosomes in the GnomAD database, including 2,322 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 0.16 (2322 hom., cov: 32)
• Consequence: ASMER1 ENST00000715910.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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+54812C>A		intron	N/A
	ASMER1	ENST00000715910.1		n.107+83963C>A		intron	N/A
	ASMER1	ENST00000850670.1		n.113+54812C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24949 AN: 151956 Hom.: 2322 Cov.: 32

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.164 AC: 24965 AN: 152074 Hom.: 2322 Cov.: 32 AF XY: 0.162 AC XY: 12018 AN XY: 74332

African (AFR) AF: 0.0953 AC: 3955 AN: 41498

American (AMR) AF: 0.130 AC: 1984 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3466

East Asian (EAS) AF: 0.142 AC: 732 AN: 5172

South Asian (SAS) AF: 0.150 AC: 725 AN: 4824

European-Finnish (FIN) AF: 0.207 AC: 2190 AN: 10568

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14129 AN: 67954

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.193 Hom.: 5072

Bravo AF: 0.156

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.54

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: rs1297214;

hg19: chr21-16331853;