rs940370

Variant names:

• chr7-105610458-G-A
• rs940370
• NM_020725.2:c.2547+71C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000295921 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATXN7L1	NM_020725.2	c.2547+71C>T		intron_variant	Intron 11 of 11	ENST00000419735.8	NP_065776.1
ATXN7L1	NM_001385596.1	c.2547+71C>T		intron_variant	Intron 11 of 11		NP_001372525.1
ATXN7L1	NM_138495.2	c.2175+71C>T		intron_variant	Intron 9 of 9		NP_612504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.2547+71C>T		intron_variant	Intron 11 of 11	1	NM_020725.2	ENSP00000410759.3
ATXN7L1	ENST00000477775.5	c.2175+71C>T		intron_variant	Intron 9 of 9	2		ENSP00000418476.1
ENSG00000295921	ENST00000733939.1	n.109-27274G>A		intron_variant	Intron 1 of 1
ENSG00000295921	ENST00000733940.1	n.257+12998G>A		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.908 AC: 24460 AN: 26948

American (AMR) AF: 0.994 AC: 31610 AN: 31812

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 22114 AN: 22114

East Asian (EAS) AF: 1.00 AC: 34480 AN: 34480

South Asian (SAS) AF: 1.00 AC: 70141 AN: 70154

European-Finnish (FIN) AF: 1.00 AC: 48206 AN: 48206

Middle Eastern (MID) AF: 0.995 AC: 5102 AN: 5128

European-Non Finnish (NFE) AF: 1.00 AC: 889139 AN: 889344

Other (OTH) AF: 0.993 AC: 50050 AN: 50382

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

African (AFR) AF: 0.907 AC: 37657 AN: 41532

American (AMR) AF: 0.989 AC: 15143 AN: 15306

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5182

South Asian (SAS) AF: 0.999 AC: 4823 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10622 AN: 10622

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68005 AN: 68032

Other (OTH) AF: 0.975 AC: 2062 AN: 2114

Alfa AF: 0.988 Hom.: 29902

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
PhyloP100		-0.58
Mutation Taster		=5/95	disease causing

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: rs940370; hg19: chr7-105250905;