rs17827966

Variant names:

• chr6-155817575-T-C
• rs17827966
• ENST00000817237.1:n.1134-2905A>G

Variant summary

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

The ENST00000817237.1(ENSG00000287092):​n.1134-2905A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,278 control chromosomes in the GnomAD database, including 1,279 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 0.12 (1279 hom., cov: 33)
• Consequence: ENSG00000287092 ENST00000817237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 3 publications found

Genes affected

ENSG00000287092 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817237.1. 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
	ENSG00000287092	ENST00000817237.1		n.1134-2905A>G		intron	N/A
	ENSG00000287092	ENST00000817238.1		n.201-5843A>G		intron	N/A
	ENSG00000287092	ENST00000817239.1		n.66+375A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18663 AN: 152160 Hom.: 1273 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.123 AC: 18694 AN: 152278 Hom.: 1279 Cov.: 33 AF XY: 0.122 AC XY: 9054 AN XY: 74448

African (AFR) AF: 0.116 AC: 4829 AN: 41568

American (AMR) AF: 0.143 AC: 2188 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3472

East Asian (EAS) AF: 0.0577 AC: 298 AN: 5162

South Asian (SAS) AF: 0.0548 AC: 265 AN: 4832

European-Finnish (FIN) AF: 0.134 AC: 1425 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8772 AN: 68012

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.124 Hom.: 651

Bravo AF: 0.127

Asia WGS AF: 0.0820 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs17827966; hg19: chr6-156138709;