dbSNP rs1477156: TACR1-AS1:n.372+45700T>C (chr2-75202015-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 NR_168009.1(TACR1-AS1):n.372+45700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,020 control chromosomes in the GnomAD database, including 27,493 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 0.57 ( 27493 hom., cov: 32)

Consequence

TACR1-AS1
NR_168009.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.207

Publications

1 publications found

Variant links:

Genes affected

TACR1-AS1 (HGNC:58209):

TACR1-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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1-AS1	NR_168009.1 link	n.372+45700T>C		intron_variant	Intron 2 of 3
TACR1-AS1	NR_168010.1 link	n.366+45700T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87260

AN:

151900

Hom.:

27454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.856

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.496

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.440

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.550

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

GnomAD4 genome

AF:

0.575

AC:

87360

AN:

152020

Hom.:

27493

Cov.:

AF XY:

0.568

AC XY:

42180

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.856

AC:

35506

AN:

41484

American (AMR)

AF:

0.496

AC:

7577

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1327

AN:

3462

East Asian (EAS)

AF:

0.409

AC:

2100

AN:

5140

South Asian (SAS)

AF:

0.408

AC:

1966

AN:

4818

European-Finnish (FIN)

AF:

0.440

AC:

4655

AN:

10578

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.481

AC:

32652

AN:

67948

Other (OTH)

AF:

0.547

AC:

1154

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1692

3383

5075

6766

8458

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.514

Hom.:

7173

Bravo

AF:

0.595

Asia WGS

AF:

0.452

AC:

1572

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.93

(source)

DANN

Benign

0.38

PhyloP100

-0.21

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