7-105760569-T-C

Variant names:

• chr7-105760569-T-C
• rs498280
• ENST00000318724.8:c.*809A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152749.3(ATXN7L1):​c.*809A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 985,398 control chromosomes in the GnomAD database, including 323,359 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 0.86 (56228 hom., cov: 33)
  • Exomes 𝑓: 0.80 (267131 hom.)
• Consequence: ATXN7L1 NM_152749.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152749.3. 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
	ATXN7L1	NM_020725.2	MANE Select	c.355+28035A>G		intron	N/A	NP_065776.1	Q9ULK2-1
	ATXN7L1	NM_152749.3		c.*809A>G		3_prime_UTR	Exon 4 of 4	NP_689962.1	Q9ULK2-2
	ATXN7L1	NM_001385596.1		c.355+28035A>G		intron	N/A	NP_001372525.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	ENST00000318724.8	TSL:1	c.*809A>G		3_prime_UTR	Exon 4 of 4	ENSP00000326344.4	Q9ULK2-2
	ATXN7L1	ENST00000419735.8	TSL:1 MANE Select	c.355+28035A>G		intron	N/A	ENSP00000410759.3	Q9ULK2-1
	ATXN7L1	ENST00000478915.1	TSL:3	c.*809A>G		3_prime_UTR	Exon 3 of 3	ENSP00000418679.1	C9IZF2

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130195 AN: 152160 Hom.: 56179 Cov.: 33

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.857

GnomAD4 exome AF: 0.800 AC: 666270 AN: 833120 Hom.: 267131 Cov.: 30 AF XY: 0.800 AC XY: 307843 AN XY: 384804

African (AFR) AF: 0.954 AC: 15063 AN: 15784

American (AMR) AF: 0.883 AC: 869 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 4498 AN: 5150

East Asian (EAS) AF: 0.971 AC: 3525 AN: 3630

South Asian (SAS) AF: 0.931 AC: 15327 AN: 16458

European-Finnish (FIN) AF: 0.856 AC: 601 AN: 702

Middle Eastern (MID) AF: 0.867 AC: 1404 AN: 1620

European-Non Finnish (NFE) AF: 0.791 AC: 602442 AN: 761508

Other (OTH) AF: 0.826 AC: 22541 AN: 27284

GnomAD4 genome AF: 0.856 AC: 130299 AN: 152278 Hom.: 56228 Cov.: 33 AF XY: 0.859 AC XY: 63985 AN XY: 74448

African (AFR) AF: 0.941 AC: 39099 AN: 41562

American (AMR) AF: 0.852 AC: 13033 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5034 AN: 5186

South Asian (SAS) AF: 0.936 AC: 4525 AN: 4832

European-Finnish (FIN) AF: 0.836 AC: 8863 AN: 10602

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53974 AN: 68010

Other (OTH) AF: 0.859 AC: 1814 AN: 2112

Alfa AF: 0.817 Hom.: 113602

Bravo AF: 0.862

Asia WGS AF: 0.939 AC: 3262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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: rs498280; hg19: chr7-105401015;