rs10567

Variant names:

• chr10-113834966-C-G
• rs10567
• NM_014881.5:c.*186G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-113834966-C-G
• chr10-113834966-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014881.5(DCLRE1A):​c.*186G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000235 in 425,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000023 (0 hom.)
• Consequence: DCLRE1A NM_014881.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 publications found

Genes affected

DCLRE1A (HGNC:17660): (DNA cross-link repair 1A) This gene encodes a conserved protein that is involved in the repair of DNA interstrand cross-links. DNA cross-links suppress transcription, replication, and DNA segregation. The encoded protein is a regulator of the mitotic cell cycle checkpoint. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014881.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCLRE1A	NM_014881.5	MANE Select	c.*186G>C		3_prime_UTR	Exon 9 of 9	NP_055696.3
	DCLRE1A	NM_001271816.2		c.*186G>C		3_prime_UTR	Exon 10 of 10	NP_001258745.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCLRE1A	ENST00000361384.7	TSL:1 MANE Select	c.*186G>C		3_prime_UTR	Exon 9 of 9	ENSP00000355185.2
	DCLRE1A	ENST00000369305.1	TSL:5	c.*186G>C		3_prime_UTR	Exon 10 of 10	ENSP00000358311.1
	DCLRE1A	ENST00000852021.1		c.*186G>C		3_prime_UTR	Exon 10 of 10	ENSP00000522080.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000235 AC: 1 AN: 425726 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 221936

African (AFR) AF: 0.00 AC: 0 AN: 10474

American (AMR) AF: 0.00 AC: 0 AN: 12412

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12146

East Asian (EAS) AF: 0.00 AC: 0 AN: 25778

South Asian (SAS) AF: 0.00 AC: 0 AN: 32810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26072

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1804

European-Non Finnish (NFE) AF: 0.00000357 AC: 1 AN: 280366

Other (OTH) AF: 0.00 AC: 0 AN: 23864

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.39
DANN	Benign	0.45
PhyloP100		-1.0

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: rs10567; hg19: chr10-115594725;