chr5-104170027-G-A

Variant names:

• chr5-104170027-G-A
• rs17156226
• ENST00000662211.1:n.548+65740G>A

Variant summary

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

The ENST00000662211.1(NIHCOLE):​n.548+65740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 152,108 control chromosomes in the GnomAD database, including 403 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 0.064 (403 hom., cov: 32)
• Consequence: NIHCOLE ENST00000662211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.156 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+65740G>A		intron_variant	Intron 4 of 5
NIHCOLE	ENST00000666145.1	n.522+65740G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0642 AC: 9758 AN: 151990 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0641 AC: 9757 AN: 152108 Hom.: 403 Cov.: 32 AF XY: 0.0650 AC XY: 4832 AN XY: 74332

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0814

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0788

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0767 Hom.: 266

Bravo AF: 0.0640

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
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: rs17156226; hg19: chr5-103505728; COSMIC: COSV60176499;