rs9909609

Variant names:

• chr17-41092091-A-G
• rs9909609
• ENST00000657137.1:n.1754A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657137.1(ENSG00000287602):​n.1754A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,680 control chromosomes in the GnomAD database, including 29,386 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 0.62 (29386 hom., cov: 31)
• Consequence: ENSG00000287602 ENST00000657137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

ENSG00000287602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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
ENSG00000287602	ENST00000657137.1	n.1754A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94031 AN: 151562 Hom.: 29358 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.620 AC: 94100 AN: 151680 Hom.: 29386 Cov.: 31 AF XY: 0.619 AC XY: 45878 AN XY: 74128

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.631

Alfa AF: 0.623 Hom.: 3636

Bravo AF: 0.617

Asia WGS AF: 0.500 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9909609; hg19: chr17-39248343;