rs4796535

Positions:

• chr17-6656544-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.0039 (0 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6656544G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C17orf100	ENST00000634977.1	n.*324+3950G>A		intron_variant		5		ENSP00000491769.1
C17orf100	ENST00000635042.1	n.*324+3950G>A		intron_variant		5		ENSP00000491523.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 565 AN: 144532 Hom.: 0 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.000800

Gnomad AMI AF: 0.00226

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.00510

Gnomad EAS AF: 0.000202

Gnomad SAS AF: 0.000870

Gnomad FIN AF: 0.000579

Gnomad MID AF: 0.00329

Gnomad NFE AF: 0.00207

Gnomad OTH AF: 0.00513

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00391 AC: 566 AN: 144642 Hom.: 0 Cov.: 27 AF XY: 0.00407 AC XY: 288 AN XY: 70692

Gnomad4 AFR AF: 0.000798

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.00510

Gnomad4 EAS AF: 0.000202

Gnomad4 SAS AF: 0.000871

Gnomad4 FIN AF: 0.000579

Gnomad4 NFE AF: 0.00207

Gnomad4 OTH AF: 0.00508

Alfa AF: 0.0113 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796535; hg19: chr17-6559863;