dbSNP rs10483217: TTLL1-AS1:n.305+1229A>G (chr22-43037998-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000733776.1(TTLL1-AS1):n.305+1229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 152,334 control chromosomes in the GnomAD database, including 83 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 0.019 ( 83 hom., cov: 33)

Consequence

TTLL1-AS1
ENST00000733776.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

Publications

0 publications found

Variant links:

Genes affected

TTLL1-AS1 (HGNC:40111): (TTLL1 antisense RNA 1)

TTLL1-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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TTLL1-AS1	ENST00000733776.1 link	n.305+1229A>G	intron_variant	Intron 2 of 2
TTLL1-AS1	ENST00000733777.1 link	n.189+1229A>G	intron_variant	Intron 2 of 2
TTLL1-AS1	ENST00000733778.1 link	n.133+1229A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0194

AC:

2959

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00321

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0849

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.0770

Gnomad SAS

AF:

0.0190

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.0311

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

GnomAD4 genome

AF:

0.0194

AC:

2962

AN:

152334

Hom.:

Cov.:

AF XY:

0.0212

AC XY:

1581

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.00320

AC:

133

AN:

41580

American (AMR)

AF:

0.0850

AC:

1300

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00317

AC:

AN:

3470

East Asian (EAS)

AF:

0.0768

AC:

398

AN:

5184

South Asian (SAS)

AF:

0.0191

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0185

AC:

196

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0112

AC:

765

AN:

68036

Other (OTH)

AF:

0.0317

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

153

307

460

614

767

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<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:

0.00718

Hom.:

Bravo

AF:

0.0233

Asia WGS

AF:

0.0530

AC:

186

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.5

(source)

DANN

Benign

0.88

PhyloP100

-0.41

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