rs17156226

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662211.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIHCOLE	ENST00000662211.1		n.548+65740G>A		intron	N/A
	NIHCOLE	ENST00000666145.1		n.522+65740G>A		intron	N/A
	NIHCOLE	ENST00000721479.1		n.522+65740G>A		intron	N/A

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

African (AFR) AF: 0.0182 AC: 756 AN: 41540

American (AMR) AF: 0.0814 AC: 1243 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3468

East Asian (EAS) AF: 0.165 AC: 853 AN: 5158

South Asian (SAS) AF: 0.0812 AC: 392 AN: 4826

European-Finnish (FIN) AF: 0.0672 AC: 711 AN: 10576

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0788 AC: 5357 AN: 67956

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0775 Hom.: 398

Bravo AF: 0.0640

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.45
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs17156226; hg19: chr5-103505728; COSMIC: COSV60176499;