rs4796537

Positions:

• chr17-6666048-G-A
• chr17-6666048-G-T

Variant summary

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

The ENST00000634558.1(ENSG00000290366):​n.510+8265G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,204 control chromosomes in the GnomAD database, including 1,489 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 0.12 (1489 hom., cov: 33)
• Consequence: ENST00000634558.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

(HGNC:):

C17orf100 (HGNC:34494): (chromosome 17 open reading frame 100)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634558.1	n.510+8265G>A		intron_variant, non_coding_transcript_variant		5
C17orf100	ENST00000634977.1	c.*324+13454G>A		intron_variant, NMD_transcript_variant		5
C17orf100	ENST00000635042.1	c.*324+13454G>A		intron_variant, NMD_transcript_variant		5
	ENST00000634823.1	n.264+7134G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17654 AN: 152086 Hom.: 1484 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.116 AC: 17680 AN: 152204 Hom.: 1489 Cov.: 33 AF XY: 0.119 AC XY: 8882 AN XY: 74420

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0301

Gnomad4 NFE AF: 0.0561

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0640 Hom.: 230

Bravo AF: 0.129

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796537; hg19: chr17-6569367;