Genetic Variant ATXN7L2:c.879+101T>A (chr1-109488566-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001350175.2(ATXN7L2):c.879+101T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,205,052 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000017 ( 0 hom. )

Consequence

ATXN7L2
NM_001350175.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.358

Publications

22 publications found

Variant links:

Genes affected

ATXN7L2 (HGNC:28713): (ataxin 7 like 2)

ATXN7L2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATXN7L2	NM_001350175.2 link	c.879+101T>A		intron_variant	Intron 6 of 10	ENST00000683729.1	NP_001337104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN7L2	ENST00000683729.1 link	c.879+101T>A		intron_variant	Intron 6 of 10		NM_001350175.2	ENSP00000507259.1		A0A804HIX1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000166

AC:

AN:

1205052

Hom.:

AF XY:

0.00000167

AC XY:

AN XY:

597692

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27348

American (AMR)

AF:

0.00

AC:

AN:

32466

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22338

East Asian (EAS)

AF:

0.00

AC:

AN:

35040

South Asian (SAS)

AF:

0.00

AC:

AN:

71920

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4264

European-Non Finnish (NFE)

AF:

0.00000219

AC:

AN:

911826

Other (OTH)

AF:

0.00

AC:

AN:

51226

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.5

(source)

DANN

Benign

0.67

PhyloP100

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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