rs12422109

chr11-3613856-C-T

Variant summary

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

The NR_164660.1(XNDC1CP):n.156-41C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 152,144 control chromosomes in the GnomAD database, including 311 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 0.044 (311 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: XNDC1CP NR_164660.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

XNDC1CP (HGNC:54662): (XRCC1 N-terminal domain containing 1, C-terminal like pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XNDC1CP	NR_164660.1	n.156-41C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XNDC1CP	ENST00000696891.1	n.156-41C>T		intron_variant, non_coding_transcript_variant
XNDC1CP	ENST00000696892.1	n.156-41C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0442 AC: 6724 AN: 152026 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.00852

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00778

Gnomad OTH AF: 0.0345

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0443 AC: 6736 AN: 152144 Hom.: 311 Cov.: 32 AF XY: 0.0436 AC XY: 3246 AN XY: 74376

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.00770

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.00778

Gnomad4 OTH AF: 0.0342

Alfa AF: 0.0165 Hom.: 84

Bravo AF: 0.0556

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	13
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12422109; hg19: chr11-3635086;