7-105808899-A-G

Position:

• chr7-105808899-A-G

Variant summary

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

The NM_020725.2(ATXN7L1):​c.251-20191T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,282 control chromosomes in the GnomAD database, including 51,718 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 0.82 (51718 hom., cov: 34)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN7L1	NM_020725.2	c.251-20191T>C		intron_variant		ENST00000419735.8	NP_065776.1
ATXN7L1	NM_001385596.1	c.251-20191T>C		intron_variant			NP_001372525.1
ATXN7L1	NM_152749.3	c.251-20191T>C		intron_variant			NP_689962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.251-20191T>C		intron_variant		1	NM_020725.2	ENSP00000410759	P1
ATXN7L1	ENST00000318724.8	c.251-20191T>C		intron_variant		1		ENSP00000326344
ATXN7L1	ENST00000478915.1	c.98-20191T>C		intron_variant		3		ENSP00000418679
ATXN7L1	ENST00000481880.5	n.285-20191T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124903 AN: 152164 Hom.: 51666 Cov.: 34

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.821 AC: 125015 AN: 152282 Hom.: 51718 Cov.: 34 AF XY: 0.819 AC XY: 60967 AN XY: 74442

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.833

Alfa AF: 0.785 Hom.: 26661

Bravo AF: 0.835

Asia WGS AF: 0.881 AC: 3063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	10
DANN	Benign	0.31

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: rs996642; hg19: chr7-105449345;