Genetic Variant TACR3-AS1:n.190-10581T>C (chr4-103580626-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000502936.1(TACR3-AS1):n.190-10581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,094 control chromosomes in the GnomAD database, including 23,173 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 0.51 ( 23173 hom., cov: 33)

Consequence

TACR3-AS1
ENST00000502936.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770

Publications

0 publications found

Variant links:

Genes affected

TACR3-AS1 (HGNC:55593): (TACR3 antisense RNA 1)

TACR3-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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR3-AS1	NR_186501.1 link	n.190-10581T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR3-AS1	ENST00000502936.1 link	n.190-10581T>C		intron_variant	Intron 2 of 4	2
TACR3-AS1	ENST00000512401.5 link	n.292-10581T>C		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77660

AN:

151976

Hom.:

23164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.756

Gnomad AMR

AF:

0.592

Gnomad ASJ

AF:

0.667

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.757

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.645

Gnomad OTH

AF:

0.535

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

GnomAD4 genome

AF:

0.511

AC:

77692

AN:

152094

Hom.:

23173

Cov.:

AF XY:

0.516

AC XY:

38337

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.189

AC:

7849

AN:

41508

American (AMR)

AF:

0.592

AC:

9047

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

2316

AN:

3472

East Asian (EAS)

AF:

0.489

AC:

2522

AN:

5160

South Asian (SAS)

AF:

0.443

AC:

2134

AN:

4818

European-Finnish (FIN)

AF:

0.757

AC:

8007

AN:

10580

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.645

AC:

43840

AN:

67960

Other (OTH)

AF:

0.536

AC:

1130

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1687

3374

5061

6748

8435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

668

1336

2004

2672

3340

<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:

0.436

Hom.:

1544

Bravo

AF:

0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.59

PhyloP100

0.077

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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