1-109488566-T-A

Variant names:

• chr1-109488566-T-A
• rs12049330
• NM_001350175.2:c.879+101T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 22 publications found

Genes affected

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

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350175.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L2	NM_001350175.2	MANE Select	c.879+101T>A		intron	N/A	NP_001337104.1	A0A804HIX1
	ATXN7L2	NM_001350174.1		c.879+101T>A		intron	N/A	NP_001337103.1	A0A804HIT1
	ATXN7L2	NM_153340.5		c.783+101T>A		intron	N/A	NP_699171.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L2	ENST00000683729.1	MANE Select	c.879+101T>A		intron	N/A	ENSP00000507259.1	A0A804HIX1
	ATXN7L2	ENST00000369870.7	TSL:1	c.783+101T>A		intron	N/A	ENSP00000358886.3	Q5T6C5
	ATXN7L2	ENST00000459635.2	TSL:2	c.879+101T>A		intron	N/A	ENSP00000507211.1	A0A804HIT1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000166 AC: 2 AN: 1205052 Hom.: 0 AF XY: 0.00000167 AC XY: 1 AN XY: 597692

African (AFR) AF: 0.00 AC: 0 AN: 27348

American (AMR) AF: 0.00 AC: 0 AN: 32466

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22338

East Asian (EAS) AF: 0.00 AC: 0 AN: 35040

South Asian (SAS) AF: 0.00 AC: 0 AN: 71920

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4264

European-Non Finnish (NFE) AF: 0.00000219 AC: 2 AN: 911826

Other (OTH) AF: 0.00 AC: 0 AN: 51226

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
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

Other links and lift over

dbSNP: rs12049330; hg19: chr1-110031188;