chr1-241889740-A-T

Variant names:

• chr1-241889740-A-T
• rs851797
• NM_130398.4:c.*140A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_130398.4(EXO1):​c.*140A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EXO1 NM_130398.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.32
• Publications: 14 publications found

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]

EXO1 Gene-Disease associations (from GenCC):

• Lynch syndrome

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130398.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXO1	NM_130398.4	MANE Select	c.*140A>T		3_prime_UTR	Exon 16 of 16	NP_569082.2
	EXO1	NM_006027.4		c.*140A>T		3_prime_UTR	Exon 14 of 14	NP_006018.4
	EXO1	NM_001319224.2		c.*140A>T		3_prime_UTR	Exon 15 of 15	NP_001306153.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXO1	ENST00000366548.8	TSL:1 MANE Select	c.*140A>T		3_prime_UTR	Exon 16 of 16	ENSP00000355506.3
	EXO1	ENST00000348581.9	TSL:1	c.*140A>T		3_prime_UTR	Exon 14 of 14	ENSP00000311873.5
	EXO1	ENST00000518483.5	TSL:1	c.*267A>T		3_prime_UTR	Exon 14 of 14	ENSP00000430251.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 658178 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 351510

African (AFR) AF: 0.00 AC: 0 AN: 16486

American (AMR) AF: 0.00 AC: 0 AN: 35298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20206

East Asian (EAS) AF: 0.00 AC: 0 AN: 32946

South Asian (SAS) AF: 0.00 AC: 0 AN: 63144

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38856

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3952

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 413508

Other (OTH) AF: 0.00 AC: 0 AN: 33782

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		2.3

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: rs851797; hg19: chr1-242053042;