NM_014881.5:c.*186G>C

Variant names:

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

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCLRE1A	NM_014881.5	c.*186G>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000361384.7	NP_055696.3
DCLRE1A	NM_001271816.2	c.*186G>C		3_prime_UTR_variant	Exon 10 of 10		NP_001258745.1
DCLRE1A	XM_006718090.2	c.*186G>C		3_prime_UTR_variant	Exon 10 of 10		XP_006718153.1
DCLRE1A	XM_011540429.2	c.*186G>C		3_prime_UTR_variant	Exon 10 of 10		XP_011538731.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCLRE1A	ENST00000361384.7	c.*186G>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_014881.5	ENSP00000355185.2
DCLRE1A	ENST00000369305.1	c.*186G>C		3_prime_UTR_variant	Exon 10 of 10	5		ENSP00000358311.1

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 v4.3

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;