rs10042854

chr5-83143876-C-T

Variant summary

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

The NM_003401.5(XRCC4):c.315+32673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,544 control chromosomes in the GnomAD database, including 18,625 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 0.48 (18625 hom., cov: 31)
• Consequence: XRCC4 NM_003401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368

Genes affected

XRCC4 (HGNC:12831): (X-ray repair cross complementing 4) The protein encoded by this gene functions together with DNA ligase IV and the DNA-dependent protein kinase in the repair of DNA double-strand breaks. This protein plays a role in both non-homologous end joining and the completion of V(D)J recombination. Mutations in this gene can cause short stature, microcephaly, and endocrine dysfunction (SSMED). Alternate transcript variants such as NM_022406 are unlikely to be expressed in some individuals due to a polymorphism (rs1805377) in the last splice acceptor site. [provided by RefSeq, Oct 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XRCC4	NM_003401.5	c.315+32673C>T		intron_variant		ENST00000396027.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XRCC4	ENST00000396027.9	c.315+32673C>T		intron_variant		5	NM_003401.5	A1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73155 AN: 151428 Hom.: 18605 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.483 AC: 73205 AN: 151544 Hom.: 18625 Cov.: 31 AF XY: 0.482 AC XY: 35666 AN XY: 74038

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.448

Alfa AF: 0.459 Hom.: 7878

Bravo AF: 0.472

Asia WGS AF: 0.377 AC: 1311 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.9
Dann	Benign	0.50

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: rs10042854; hg19: chr5-82439695;