8-18123580-C-T

Variant names:

• chr8-18123580-C-T
• rs17126237
• ENST00000659561.1:n.216-3260C>T

Variant summary

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

The ENST00000659561.1(ENSG00000286542):​n.216-3260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,080 control chromosomes in the GnomAD database, including 2,991 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 0.17 (2991 hom., cov: 31)
• Consequence: ENSG00000286542 ENST00000659561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

ENSG00000286542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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
ENSG00000286542	ENST00000659561.1	n.216-3260C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26194 AN: 151964 Hom.: 2970 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.173 AC: 26263 AN: 152080 Hom.: 2991 Cov.: 31 AF XY: 0.174 AC XY: 12953 AN XY: 74362

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0324

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.168

Alfa AF: 0.114 Hom.: 782

Bravo AF: 0.179

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17126237; hg19: chr8-17981089;