rs10057194

chr5-83362752-A-Gchr5-83362752-A-T

Variant summary

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

The XM_017009827.3(XRCC4):c.894-7515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,114 control chromosomes in the GnomAD database, including 3,339 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 0.15 (3339 hom., cov: 32)
• Consequence: XRCC4 XM_017009827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

XRCC4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XRCC4	XM_017009827.3	c.894-7515A>G		intron_variant
XRCC4	XM_047417695.1	c.894-7515A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23471 AN: 151996 Hom.: 3315 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0517

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0521

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.155 AC: 23542 AN: 152114 Hom.: 3339 Cov.: 32 AF XY: 0.152 AC XY: 11314 AN XY: 74362

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.0521

Gnomad4 OTH AF: 0.127

Alfa AF: 0.108 Hom.: 272

Bravo AF: 0.172

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.24
Dann	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10057194; hg19: chr5-82658571; COSMIC: COSV60160631;