rs516802

Variant names:

• chr7-105744220-T-C
• rs516802
• NM_020725.2:c.355+44384A>G

Variant summary

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

The NM_001385596.1(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_001385596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385596.1. 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+44384A>G		intron	N/A	NP_065776.1
	ATXN7L1	NM_001385596.1		c.355+44384A>G		intron	N/A	NP_001372525.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	ENST00000419735.8	TSL:1 MANE Select	c.355+44384A>G		intron	N/A	ENSP00000410759.3

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

African (AFR) AF: 0.396 AC: 16383 AN: 41412

American (AMR) AF: 0.198 AC: 3028 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3466

East Asian (EAS) AF: 0.459 AC: 2370 AN: 5160

South Asian (SAS) AF: 0.305 AC: 1466 AN: 4810

European-Finnish (FIN) AF: 0.171 AC: 1813 AN: 10574

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8605 AN: 67990

Other (OTH) AF: 0.220 AC: 464 AN: 2110

Alfa AF: 0.154 Hom.: 3431

Bravo AF: 0.240

Asia WGS AF: 0.357 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.077
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: rs516802; hg19: chr7-105384666;