rs7711825

Variant names:

• chr5-83225799-C-A
• rs7711825
• NM_003401.5:c.745+20878C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-83225799-C-A
• chr5-83225799-C-G
• chr5-83225799-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003401.5(XRCC4):​c.745+20878C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,242 control chromosomes in the GnomAD database, including 9,776 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 0.27 (9776 hom., cov: 30)
• Consequence: XRCC4 NM_003401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 6 publications found

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]

XRCC4 Gene-Disease associations (from GenCC):

• short stature, microcephaly, and endocrine dysfunction

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Laboratory for Molecular Medicine
• microcephalic primordial dwarfism-insulin resistance syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003401.5. 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
	XRCC4	NM_003401.5	MANE Select	c.745+20878C>A		intron	N/A	NP_003392.1
	XRCC4	NM_001318012.3		c.745+20878C>A		intron	N/A	NP_001304941.1
	XRCC4	NM_022406.5		c.745+20878C>A		intron	N/A	NP_071801.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XRCC4	ENST00000396027.9	TSL:5 MANE Select	c.745+20878C>A		intron	N/A	ENSP00000379344.4
	XRCC4	ENST00000511817.1	TSL:1	c.745+20878C>A		intron	N/A	ENSP00000421491.1
	XRCC4	ENST00000282268.7	TSL:1	c.745+20878C>A		intron	N/A	ENSP00000282268.3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40542 AN: 151124 Hom.: 9750 Cov.: 30

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.269 AC: 40623 AN: 151242 Hom.: 9776 Cov.: 30 AF XY: 0.273 AC XY: 20135 AN XY: 73794

African (AFR) AF: 0.605 AC: 24948 AN: 41222

American (AMR) AF: 0.290 AC: 4391 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3458

East Asian (EAS) AF: 0.649 AC: 3314 AN: 5110

South Asian (SAS) AF: 0.211 AC: 1007 AN: 4778

European-Finnish (FIN) AF: 0.128 AC: 1336 AN: 10470

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0689 AC: 4671 AN: 67796

Other (OTH) AF: 0.242 AC: 506 AN: 2088

Alfa AF: 0.133 Hom.: 12514

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.34
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism (auto)

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: rs7711825; hg19: chr5-82521618;