rs4419569

Variant names:

• chr5-104165540-A-C
• rs4419569
• ENST00000662211.1:n.548+61253A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-104165540-A-C
• chr5-104165540-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000662211.1(NIHCOLE):​n.548+61253A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,090 control chromosomes in the GnomAD database, including 53,981 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 0.84 (53981 hom., cov: 32)
• Consequence: NIHCOLE ENST00000662211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

NIHCOLE (HGNC:53024): (ncRNA involved in NHEJ oncogenic ligation efficiency)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIHCOLE	ENST00000662211.1	n.548+61253A>C		intron_variant	Intron 4 of 5
NIHCOLE	ENST00000666145.1	n.522+61253A>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126920 AN: 151972 Hom.: 53940 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.835 AC: 127012 AN: 152090 Hom.: 53981 Cov.: 32 AF XY: 0.824 AC XY: 61226 AN XY: 74320

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.827

Alfa AF: 0.874 Hom.: 6832

Bravo AF: 0.828

Asia WGS AF: 0.523 AC: 1818 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	16
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4419569; hg19: chr5-103501241;