rs1635501

Positions:

• chr1-241877473-C-T

Variant summary

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

The NM_130398.4(EXO1):​c.1515-1276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,858 control chromosomes in the GnomAD database, including 22,658 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 0.54 (22658 hom., cov: 31)
• Consequence: EXO1 NM_130398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

Genes affected

EXO1 (HGNC:3511): (exonuclease 1) This gene encodes a protein with 5' to 3' exonuclease activity as well as an RNase H activity. It is similar to the Saccharomyces cerevisiae protein Exo1 which interacts with Msh2 and which is involved in mismatch repair and recombination. Alternative splicing of this gene results in three transcript variants encoding two different isoforms. [provided by RefSeq, Jul 2008]

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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EXO1	NM_130398.4	c.1515-1276C>T		intron_variant		ENST00000366548.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXO1	ENST00000366548.8	c.1515-1276C>T		intron_variant		1	NM_130398.4	P2
EXO1	ENST00000348581.9	c.1515-1276C>T		intron_variant		1		P2
EXO1	ENST00000518483.5	c.1515-1276C>T		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82042 AN: 151740 Hom.: 22623 Cov.: 31

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.541 AC: 82135 AN: 151858 Hom.: 22658 Cov.: 31 AF XY: 0.547 AC XY: 40574 AN XY: 74236

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.558

Alfa AF: 0.539 Hom.: 24039

Bravo AF: 0.545

Asia WGS AF: 0.655 AC: 2277 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	0.63
DANN	Benign	0.64

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: rs1635501; hg19: chr1-242040775;