rs879606

Variant names:

• chr17-39625596-A-G
• rs879606
• ENST00000815498.1:n.42+2765T>C

Variant summary

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

The ENST00000815498.1(ENSG00000306125):​n.42+2765T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 151,996 control chromosomes in the GnomAD database, including 41,352 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 0.73 (41352 hom., cov: 32)
• Consequence: ENSG00000306125 ENST00000815498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 50 publications found

Genes affected

ENSG00000306125 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 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
ENSG00000306125	ENST00000815498.1	n.42+2765T>C		intron_variant	Intron 1 of 1
ENSG00000306125	ENST00000815499.1	n.86+2765T>C		intron_variant	Intron 1 of 1
ENSG00000306125	ENST00000815500.1	n.200+1911T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110570 AN: 151878 Hom.: 41325 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.728 AC: 110661 AN: 151996 Hom.: 41352 Cov.: 32 AF XY: 0.725 AC XY: 53812 AN XY: 74274

African (AFR) AF: 0.578 AC: 23943 AN: 41408

American (AMR) AF: 0.692 AC: 10578 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2915 AN: 3466

East Asian (EAS) AF: 0.445 AC: 2292 AN: 5154

South Asian (SAS) AF: 0.764 AC: 3687 AN: 4824

European-Finnish (FIN) AF: 0.814 AC: 8619 AN: 10582

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56053 AN: 67960

Other (OTH) AF: 0.749 AC: 1578 AN: 2106

Alfa AF: 0.803 Hom.: 82788

Bravo AF: 0.711

Asia WGS AF: 0.668 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs879606; hg19: chr17-37781849;