7-105613918-G-T

Variant names:

• chr7-105613918-G-T
• rs1490376676
• NM_020725.2:c.2416C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020725.2(ATXN7L1):​c.2416C>A​(p.Pro806Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000143 in 1,399,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ATXN7L1 NM_020725.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.16

Genes affected

ATXN7L1 (HGNC:22210): (ataxin 7 like 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09069714).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATXN7L1	NM_020725.2	c.2416C>A	p.Pro806Thr	missense_variant	Exon 10 of 12	ENST00000419735.8	NP_065776.1
ATXN7L1	NM_001385596.1	c.2416C>A	p.Pro806Thr	missense_variant	Exon 10 of 12		NP_001372525.1
ATXN7L1	NM_138495.2	c.2044C>A	p.Pro682Thr	missense_variant	Exon 8 of 10		NP_612504.1
ATXN7L1	NM_001318229.2	c.1768C>A	p.Pro590Thr	missense_variant	Exon 10 of 10		NP_001305158.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.2416C>A	p.Pro806Thr	missense_variant	Exon 10 of 12	1	NM_020725.2	ENSP00000410759.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1399796 Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1 AN XY: 690364

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000185

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.058
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	18
DANN	Benign	0.86
DEOGEN2	Benign	0.0083	T;.;T;T
Eigen	Benign	-0.20
Eigen_PC	Benign	0.011
FATHMM_MKL	Benign	0.63	D
LIST_S2	Benign	0.83	T;T;T;T
M_CAP	Benign	0.0014	T
MetaRNN	Benign	0.091	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.77	N;.;.;.
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-0.90	N;N;N;N
REVEL	Benign	0.041
Sift	Benign	0.39	T;T;T;T
Sift4G	Benign	0.37	T;T;T;T
Polyphen		0.0	B;B;.;.
Vest4		0.19
MutPred		0.19		Loss of catalytic residue at P806 (P = 0.007);.;.;.;
MVP		0.46
MPC		0.47
ClinPred		0.65	D
GERP RS		4.9
Varity_R		0.12
gMVP		0.33

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

LitVar

Other links and lift over

dbSNP: rs1490376676; hg19: chr7-105254365;