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. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
NIHCOLE	ENST00000721479.1	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

African (AFR) AF: 0.872 AC: 36180 AN: 41510

American (AMR) AF: 0.730 AC: 11152 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1951 AN: 5164

South Asian (SAS) AF: 0.699 AC: 3371 AN: 4826

European-Finnish (FIN) AF: 0.805 AC: 8498 AN: 10552

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60571 AN: 67974

Other (OTH) AF: 0.827 AC: 1746 AN: 2110

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4419569; hg19: chr5-103501241;