rs17466684

Variant names:

• chr8-27595330-G-A
• rs17466684
• ENST00000774578.1:n.170-1737G>A

Variant summary

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

The ENST00000774578.1(ENSG00000300853):​n.170-1737G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,068 control chromosomes in the GnomAD database, including 2,074 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 0.15 (2074 hom., cov: 32)
• Consequence: ENSG00000300853 ENST00000774578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 27 publications found

Genes affected

ENSG00000300853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901919	XR_007060868.1	n.1398-1737G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300853	ENST00000774578.1	n.170-1737G>A		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774579.1	n.285-1737G>A		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774580.1	n.129-1737G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22799 AN: 151950 Hom.: 2064 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.150 AC: 22824 AN: 152068 Hom.: 2074 Cov.: 32 AF XY: 0.154 AC XY: 11450 AN XY: 74304

African (AFR) AF: 0.0555 AC: 2305 AN: 41526

American (AMR) AF: 0.219 AC: 3345 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.147 AC: 757 AN: 5152

South Asian (SAS) AF: 0.154 AC: 740 AN: 4812

European-Finnish (FIN) AF: 0.241 AC: 2538 AN: 10544

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12292 AN: 67972

Other (OTH) AF: 0.138 AC: 291 AN: 2112

Alfa AF: 0.162 Hom.: 4630

Bravo AF: 0.143

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17466684; hg19: chr8-27452847;