rs17827067

Variant names:

• chr8-60882612-C-T
• rs17827067
• ENST00000668199.1:n.604-2386C>T

Variant summary

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

The ENST00000668199.1(ENSG00000287975):​n.604-2386C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 152,212 control chromosomes in the GnomAD database, including 498 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 0.077 (498 hom., cov: 32)
• Consequence: ENSG00000287975 ENST00000668199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 2 publications found

Genes affected

ENSG00000287975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668199.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287975	ENST00000668199.1		n.604-2386C>T		intron	N/A
	ENSG00000287975	ENST00000829534.1		n.114-2386C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11760 AN: 152094 Hom.: 498 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0364

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0773 AC: 11769 AN: 152212 Hom.: 498 Cov.: 32 AF XY: 0.0753 AC XY: 5606 AN XY: 74410

African (AFR) AF: 0.0978 AC: 4060 AN: 41514

American (AMR) AF: 0.0614 AC: 940 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0364 AC: 126 AN: 3466

East Asian (EAS) AF: 0.0343 AC: 178 AN: 5188

South Asian (SAS) AF: 0.0515 AC: 248 AN: 4818

European-Finnish (FIN) AF: 0.0598 AC: 633 AN: 10588

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5318 AN: 68020

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0734 Hom.: 186

Bravo AF: 0.0796

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.69
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17827067; hg19: chr8-61795171;