chr17-41092091-A-G

Position:

• chr17-41092091-A-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/exons	MANE	Protein	UniProt
		n.41092091A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287602	ENST00000657137.1	n.1754A>G		non_coding_transcript_exon_variant	1/2

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;