15-66930806-C-T

Variant names:

• chr15-66930806-C-T
• rs7168889
• ENST00000559904.1:n.111-637C>T

Variant summary

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

The ENST00000559904.1(ENSG00000259437):​n.111-637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,074 control chromosomes in the GnomAD database, including 15,071 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 0.42 (15071 hom., cov: 33)
• Consequence: ENSG00000259437 ENST00000559904.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913

Genes affected

ENSG00000259437 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 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
ENSG00000259437	ENST00000559904.1	n.111-637C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63818 AN: 151956 Hom.: 15056 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.420 AC: 63857 AN: 152074 Hom.: 15071 Cov.: 33 AF XY: 0.430 AC XY: 31947 AN XY: 74312

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.476

Alfa AF: 0.463 Hom.: 19456

Bravo AF: 0.409

Asia WGS AF: 0.596 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7168889; hg19: chr15-67223144;