17-4375540-A-G

Variant names:

• chr17-4375540-A-G
• rs9906760
• ENST00000808430.1:n.489+8254A>G

Variant summary

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

The ENST00000808430.1(ENSG00000305082):​n.489+8254A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,876 control chromosomes in the GnomAD database, including 15,256 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 0.43 (15256 hom., cov: 31)
• Consequence: ENSG00000305082 ENST00000808430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 12 publications found

Genes affected

ENSG00000305082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808430.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305082	ENST00000808430.1		n.489+8254A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64597 AN: 151758 Hom.: 15206 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.426 AC: 64707 AN: 151876 Hom.: 15256 Cov.: 31 AF XY: 0.426 AC XY: 31582 AN XY: 74214

African (AFR) AF: 0.641 AC: 26550 AN: 41400

American (AMR) AF: 0.422 AC: 6424 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5182

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4818

European-Finnish (FIN) AF: 0.379 AC: 3985 AN: 10520

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22549 AN: 67952

Other (OTH) AF: 0.401 AC: 845 AN: 2106

Alfa AF: 0.365 Hom.: 31219

Bravo AF: 0.440

Asia WGS AF: 0.347 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.73
DANN	Benign	0.76
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9906760; hg19: chr17-4278835;