17-70882346-A-G

Variant names:

• chr17-70882346-A-G
• rs1015657
• ENST00000774266.1:n.247-15326A>G

Variant summary

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

The ENST00000774266.1(ENSG00000300827):​n.247-15326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,106 control chromosomes in the GnomAD database, including 23,541 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 0.54 (23541 hom., cov: 33)
• Consequence: ENSG00000300827 ENST00000774266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687
• Publications: 4 publications found

Genes affected

ENSG00000300827 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774266.1. 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
	ENSG00000300827	ENST00000774266.1		n.247-15326A>G		intron	N/A
	ENSG00000300827	ENST00000774267.1		n.186-15326A>G		intron	N/A
	ENSG00000300827	ENST00000774268.1		n.105-132A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82515 AN: 151988 Hom.: 23521 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.543 AC: 82584 AN: 152106 Hom.: 23541 Cov.: 33 AF XY: 0.544 AC XY: 40468 AN XY: 74324

African (AFR) AF: 0.665 AC: 27614 AN: 41506

American (AMR) AF: 0.551 AC: 8415 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2067 AN: 3472

East Asian (EAS) AF: 0.900 AC: 4644 AN: 5158

South Asian (SAS) AF: 0.523 AC: 2525 AN: 4828

European-Finnish (FIN) AF: 0.441 AC: 4667 AN: 10574

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30785 AN: 67976

Other (OTH) AF: 0.537 AC: 1133 AN: 2108

Alfa AF: 0.488 Hom.: 72026

Bravo AF: 0.564

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1015657; hg19: chr17-68878487;