17-39625357-G-C

Variant names:

• chr17-39625357-G-C
• rs4795390
• ENST00000815498.1:n.42+3004C>G

Variant summary

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

The ENST00000815498.1(ENSG00000306125):​n.42+3004C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,002 control chromosomes in the GnomAD database, including 44,800 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 0.76 (44800 hom., cov: 31)
• Consequence: ENSG00000306125 ENST00000815498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 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+3004C>G		intron_variant	Intron 1 of 1
ENSG00000306125	ENST00000815499.1	n.86+3004C>G		intron_variant	Intron 1 of 1
ENSG00000306125	ENST00000815500.1	n.200+2150C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115895 AN: 151884 Hom.: 44747 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.763 AC: 116015 AN: 152002 Hom.: 44800 Cov.: 31 AF XY: 0.759 AC XY: 56349 AN XY: 74282

African (AFR) AF: 0.700 AC: 28957 AN: 41390

American (AMR) AF: 0.704 AC: 10765 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2915 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2301 AN: 5132

South Asian (SAS) AF: 0.766 AC: 3693 AN: 4824

European-Finnish (FIN) AF: 0.814 AC: 8621 AN: 10590

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 56115 AN: 67994

Other (OTH) AF: 0.781 AC: 1650 AN: 2112

Alfa AF: 0.742 Hom.: 2298

Bravo AF: 0.751

Asia WGS AF: 0.686 AC: 2387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4795390; hg19: chr17-37781610;