1-109488566-T-G

Variant names:

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

Variant summary

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

The NM_001350175.2(ATXN7L2):​c.879+101T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,356,094 control chromosomes in the GnomAD database, including 17,802 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 0.13 (1640 hom., cov: 33)
  • Exomes 𝑓: 0.16 (16162 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATXN7L2	NM_001350175.2	c.879+101T>G		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	c.879+101T>G		intron_variant	Intron 6 of 10		NM_001350175.2	ENSP00000507259.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19706 AN: 152084 Hom.: 1642 Cov.: 33

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.158 AC: 190608 AN: 1203892 Hom.: 16162 AF XY: 0.159 AC XY: 95143 AN XY: 597196

African (AFR) AF: 0.0306 AC: 838 AN: 27342

American (AMR) AF: 0.176 AC: 5710 AN: 32442

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 4574 AN: 22312

East Asian (EAS) AF: 0.299 AC: 10489 AN: 35032

South Asian (SAS) AF: 0.184 AC: 13199 AN: 71872

European-Finnish (FIN) AF: 0.170 AC: 8246 AN: 48608

Middle Eastern (MID) AF: 0.147 AC: 628 AN: 4260

European-Non Finnish (NFE) AF: 0.152 AC: 138569 AN: 910836

Other (OTH) AF: 0.163 AC: 8355 AN: 51188

GnomAD4 genome AF: 0.129 AC: 19709 AN: 152202 Hom.: 1640 Cov.: 33 AF XY: 0.132 AC XY: 9796 AN XY: 74406

African (AFR) AF: 0.0347 AC: 1443 AN: 41550

American (AMR) AF: 0.137 AC: 2103 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3464

East Asian (EAS) AF: 0.308 AC: 1593 AN: 5172

South Asian (SAS) AF: 0.183 AC: 881 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1885 AN: 10590

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10504 AN: 67994

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.147 Hom.: 5095

Bravo AF: 0.126

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.62
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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; COSMIC: COSV63992608; COSMIC: COSV63992608;