rs17178527

Variant names:

• chr6-141584943-G-A
• rs17178527
• ENST00000847688.1:n.205+4866G>A

Variant summary

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

The ENST00000847688.1(ENSG00000310155):​n.205+4866G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,452 control chromosomes in the GnomAD database, including 1,164 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 (1164 hom., cov: 32)
• Consequence: ENSG00000310155 ENST00000847688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 9 publications found

Genes affected

ENSG00000310155 (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 (EAS) allele frequency at 95% confidence interval = 0.187 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
ENSG00000310155	ENST00000847688.1	n.205+4866G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18043 AN: 151334 Hom.: 1163 Cov.: 32

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18043 AN: 151452 Hom.: 1164 Cov.: 32 AF XY: 0.119 AC XY: 8783 AN XY: 74004

African (AFR) AF: 0.0637 AC: 2642 AN: 41446

American (AMR) AF: 0.118 AC: 1785 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0796 AC: 276 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1022 AN: 5174

South Asian (SAS) AF: 0.101 AC: 486 AN: 4814

European-Finnish (FIN) AF: 0.184 AC: 1915 AN: 10434

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.142 AC: 9608 AN: 67624

Other (OTH) AF: 0.119 AC: 250 AN: 2102

Alfa AF: 0.122 Hom.: 220

Bravo AF: 0.112

Asia WGS AF: 0.159 AC: 544 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs17178527; hg19: chr6-141906080; COSMIC: COSV68647625;