ENST00000450287.2:n.244+30973T>C

Variant names:

• chr10-44892108-A-G
• rs1977584
• ENST00000450287.2:n.244+30973T>C

Variant summary

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

The ENST00000450287.2(TMEM72-AS1):​n.244+30973T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,200 control chromosomes in the GnomAD database, including 52,935 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 0.83 (52935 hom., cov: 34)
• Consequence: TMEM72-AS1 ENST00000450287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 0 publications found

Genes affected

TMEM72-AS1 (HGNC:27349): (TMEM72 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450287.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM72-AS1	NR_033842.1		n.244+30973T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM72-AS1	ENST00000450287.2	TSL:2	n.244+30973T>C		intron	N/A
	TMEM72-AS1	ENST00000656140.1		n.178-6808T>C		intron	N/A
	TMEM72-AS1	ENST00000657040.1		n.124-6808T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126568 AN: 152082 Hom.: 52896 Cov.: 34

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.832 AC: 126658 AN: 152200 Hom.: 52935 Cov.: 34 AF XY: 0.836 AC XY: 62179 AN XY: 74376

African (AFR) AF: 0.757 AC: 31451 AN: 41520

American (AMR) AF: 0.852 AC: 13032 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2942 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4729 AN: 5194

South Asian (SAS) AF: 0.898 AC: 4325 AN: 4816

European-Finnish (FIN) AF: 0.897 AC: 9479 AN: 10570

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.852 AC: 57918 AN: 68006

Other (OTH) AF: 0.827 AC: 1749 AN: 2114

Alfa AF: 0.830 Hom.: 2690

Bravo AF: 0.823

Asia WGS AF: 0.897 AC: 3120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1977584; hg19: chr10-45387556;