rs516802

Positions:

• chr7-105744220-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020725.2(ATXN7L1):​c.355+44384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,012 control chromosomes in the GnomAD database, including 5,172 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 0.23 (5172 hom., cov: 32)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATXN7L1	NM_020725.2	c.355+44384A>G		intron_variant		ENST00000419735.8
ATXN7L1	NM_001385596.1	c.355+44384A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.355+44384A>G		intron_variant		1	NM_020725.2	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35039 AN: 151894 Hom.: 5171 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.216

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.231 AC: 35056 AN: 152012 Hom.: 5172 Cov.: 32 AF XY: 0.234 AC XY: 17396 AN XY: 74306

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.220

Alfa AF: 0.151 Hom.: 2769

Bravo AF: 0.240

Asia WGS AF: 0.357 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.52

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: rs516802; hg19: chr7-105384666;