rs4796049

Positions:

• chr17-35189896-A-C

Variant summary

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

The variant allele was found at a frequency of 0.0925 in 151,762 control chromosomes in the GnomAD database, including 813 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 0.093 (813 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35189896A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266981	ENST00000590144.1	n.116-1004A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14007 AN: 151642 Hom.: 809 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0925

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

GnomAD4 genome AF: 0.0925 AC: 14041 AN: 151762 Hom.: 813 Cov.: 32 AF XY: 0.0981 AC XY: 7281 AN XY: 74200

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.0929

Alfa AF: 0.0828 Hom.: 86

Bravo AF: 0.0968

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.8
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796049; hg19: chr17-33516915;