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 ENST00000635042.1(C17orf100):​n.*324+13454G>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: C17orf100 ENST00000635042.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635042.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290366	ENST00000634558.1	TSL:5	n.510+8265G>A		intron	N/A
	ENSG00000290366	ENST00000634823.1	TSL:5	n.264+7134G>A		intron	N/A
	C17orf100	ENST00000634977.1	TSL:5	n.*324+13454G>A		intron	N/A	ENSP00000491769.1	A0A1W2PPW6

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4796537;

hg19: chr17-6569367;