ENST00000430391.1:n.239+7437C>T

Variant names:

• chr21-14926209-C-T
• rs17274722
• ENST00000430391.1:n.239+7437C>T

Variant summary

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

The ENST00000430391.1(ENSG00000235277):​n.239+7437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0662 in 152,164 control chromosomes in the GnomAD database, including 432 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 0.066 (432 hom., cov: 32)
• Consequence: ENSG00000235277 ENST00000430391.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 2 publications found

Genes affected

ENSG00000235277 (HGNC:):

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235277	ENST00000430391.1	n.239+7437C>T		intron_variant	Intron 1 of 1	2
ASMER1	ENST00000432230.6	n.88-68501G>A		intron_variant	Intron 1 of 3	5
ASMER1	ENST00000715452.1	n.173+1134G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10072 AN: 152046 Hom.: 432 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0787

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

GnomAD4 genome AF: 0.0662 AC: 10077 AN: 152164 Hom.: 432 Cov.: 32 AF XY: 0.0651 AC XY: 4842 AN XY: 74382

African (AFR) AF: 0.0194 AC: 805 AN: 41502

American (AMR) AF: 0.103 AC: 1580 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0478 AC: 230 AN: 4814

European-Finnish (FIN) AF: 0.0639 AC: 677 AN: 10594

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0881 AC: 5991 AN: 68002

Other (OTH) AF: 0.0779 AC: 164 AN: 2106

Alfa AF: 0.0772 Hom.: 285

Bravo AF: 0.0705

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17274722; hg19: chr21-16298530;