rs940370

Positions:

• chr7-105610458-G-A
• chr7-105610458-G-C

Variant summary

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

The NM_020725.2(ATXN7L1):​c.2547+71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 1,330,862 control chromosomes in the GnomAD database, including 658,337 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 0.97 (72199 hom., cov: 32)
  • Exomes 𝑓: 1.0 (586138 hom.)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATXN7L1	NM_020725.2	c.2547+71C>T		intron_variant		ENST00000419735.8
ATXN7L1	NM_001385596.1	c.2547+71C>T		intron_variant
ATXN7L1	NM_138495.2	c.2175+71C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.2547+71C>T		intron_variant		1	NM_020725.2	P1
ATXN7L1	ENST00000477775.5	c.2175+71C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.973 AC: 148054 AN: 152176 Hom.: 72143 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.989

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.975

GnomAD4 exome AF: 0.997 AC: 1175302 AN: 1178568 Hom.: 586138 AF XY: 0.998 AC XY: 586354 AN XY: 587748

Gnomad4 AFR exome AF: 0.908

Gnomad4 AMR exome AF: 0.994

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.993

GnomAD4 genome AF: 0.973 AC: 148169 AN: 152294 Hom.: 72199 Cov.: 32 AF XY: 0.974 AC XY: 72551 AN XY: 74472

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.989

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.999

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.975

Alfa AF: 0.983 Hom.: 9145

Bravo AF: 0.969

Asia WGS AF: 0.995 AC: 3460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.22

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: rs940370; hg19: chr7-105250905;