rs17612678

Variant names:

• chr15-93271900-T-C
• rs17612678
• ENST00000667030.1:n.236+12663T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667030.1(ENSG00000257060):​n.236+12663T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,990 control chromosomes in the GnomAD database, including 8,101 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 0.29 (8101 hom., cov: 31)
• Consequence: ENSG00000257060 ENST00000667030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 14 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667030.1. 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
	ENSG00000257060	ENST00000667030.1		n.236+12663T>C		intron	N/A
	ENSG00000257060	ENST00000791023.1		n.533+40048T>C		intron	N/A
	ENSG00000257060	ENST00000791024.1		n.90+40048T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43570 AN: 151872 Hom.: 8097 Cov.: 31

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0436

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.287 AC: 43566 AN: 151990 Hom.: 8101 Cov.: 31 AF XY: 0.284 AC XY: 21120 AN XY: 74294

African (AFR) AF: 0.0732 AC: 3036 AN: 41480

American (AMR) AF: 0.288 AC: 4390 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3464

East Asian (EAS) AF: 0.0439 AC: 227 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4812

European-Finnish (FIN) AF: 0.415 AC: 4371 AN: 10536

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28111 AN: 67942

Other (OTH) AF: 0.293 AC: 620 AN: 2114

Alfa AF: 0.362 Hom.: 43281

Bravo AF: 0.266

Asia WGS AF: 0.144 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.0
DANN	Benign	0.83
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs17612678; hg19: chr15-93815129;