Genetic Variant NR_168009.1:n.372+44955G>A (chr2-75201270-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NR_168009.1(TACR1-AS1):n.372+44955G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.068 ( 357 hom., cov: 20)

Failed GnomAD Quality Control

Consequence

TACR1-AS1
NR_168009.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.568

Publications

2 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1-AS1	NR_168009.1 link	n.372+44955G>A		intron_variant	Intron 2 of 3
TACR1-AS1	NR_168010.1 link	n.366+44955G>A		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0678

AC:

8930

AN:

131718

Hom.:

358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0572

Gnomad AMI

AF:

0.0251

Gnomad AMR

AF:

0.0439

Gnomad ASJ

AF:

0.0373

Gnomad EAS

AF:

0.0102

Gnomad SAS

AF:

0.0392

Gnomad FIN

AF:

0.0647

Gnomad MID

AF:

0.0880

Gnomad NFE

AF:

0.0861

Gnomad OTH

AF:

0.0699

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0678

AC:

8933

AN:

131842

Hom.:

357

Cov.:

AF XY:

0.0662

AC XY:

4186

AN XY:

63234

show subpopulations

African (AFR)

AF:

0.0572

AC:

2058

AN:

35958

American (AMR)

AF:

0.0438

AC:

566

AN:

12932

Ashkenazi Jewish (ASJ)

AF:

0.0373

AC:

120

AN:

3218

East Asian (EAS)

AF:

0.0102

AC:

AN:

3630

South Asian (SAS)

AF:

0.0396

AC:

132

AN:

3336

European-Finnish (FIN)

AF:

0.0647

AC:

484

AN:

7478

Middle Eastern (MID)

AF:

0.0720

AC:

AN:

264

European-Non Finnish (NFE)

AF:

0.0861

AC:

5368

AN:

62370

Other (OTH)

AF:

0.0703

AC:

128

AN:

1820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.650

Heterozygous variant carriers

360

720

1081

1441

1801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0671

Hom.:

Bravo

AF:

0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.33

(source)

DANN

Benign

0.21

PhyloP100

-0.57

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