dbSNP rs7911712: TMEM72-AS1:n.2042-918C>T (chr10-44824206-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000450287.2(TMEM72-AS1):n.2042-918C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,092 control chromosomes in the GnomAD database, including 1,143 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 0.11 ( 1143 hom., cov: 33)

Consequence

TMEM72-AS1
ENST00000450287.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.631

Publications

8 publications found

Variant links:

Genes affected

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

TMEM72-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM72-AS1	NR_033842.1 link	n.2042-918C>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TMEM72-AS1	ENST00000450287.2 link	n.2042-918C>T	intron_variant	Intron 6 of 7	2
TMEM72-AS1	ENST00000657040.1 link	n.217-28665C>T	intron_variant	Intron 2 of 2
TMEM72-AS1	ENST00000659078.1 link	n.2343-918C>T	intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17439

AN:

151974

Hom.:

1143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0852

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.0766

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0611

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.101

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

GnomAD4 genome

AF:

0.115

AC:

17460

AN:

152092

Hom.:

1143

Cov.:

AF XY:

0.112

AC XY:

8357

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.0856

AC:

3555

AN:

41532

American (AMR)

AF:

0.0765

AC:

1170

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

555

AN:

3466

East Asian (EAS)

AF:

0.000967

AC:

AN:

5170

South Asian (SAS)

AF:

0.0607

AC:

293

AN:

4824

European-Finnish (FIN)

AF:

0.139

AC:

1463

AN:

10556

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9990

AN:

67954

Other (OTH)

AF:

0.0996

AC:

210

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

775

1551

2326

3102

3877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.131

Hom.:

4182

Bravo

AF:

0.108

Asia WGS

AF:

0.0350

AC:

122

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.27

(source)

DANN

Benign

0.46

PhyloP100

-0.63

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over