rs4796537

Variant names:

• chr17-6666048-G-A
• rs4796537
• ENST00000634558.1:n.510+8265G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634558.1(ENSG00000290366):​n.510+8265G>A variant causes a intron 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: ENSG00000290366 ENST00000634558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 1 publications found

Genes affected

ENSG00000290366 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290366	ENST00000634558.1	n.510+8265G>A		intron_variant	Intron 2 of 3	5
ENSG00000290366	ENST00000634823.1	n.264+7134G>A		intron_variant	Intron 2 of 2	5
C17orf100	ENST00000634977.1	n.*324+13454G>A		intron_variant	Intron 1 of 1	5		ENSP00000491769.1
C17orf100	ENST00000635042.1	n.*324+13454G>A		intron_variant	Intron 1 of 1	5		ENSP00000491523.1

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

African (AFR) AF: 0.183 AC: 7607 AN: 41506

American (AMR) AF: 0.175 AC: 2681 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5170

South Asian (SAS) AF: 0.170 AC: 820 AN: 4828

European-Finnish (FIN) AF: 0.0301 AC: 319 AN: 10606

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0561 AC: 3812 AN: 68010

Other (OTH) AF: 0.113 AC: 238 AN: 2114

Alfa AF: 0.0801 Hom.: 546

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4796537; hg19: chr17-6569367;