rs4796535

Variant names:

• chr17-6656544-G-A
• rs4796535
• ENST00000634977.1:n.*324+3950G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000635042.1(C17orf100):​n.*324+3950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: C17orf100 ENST00000635042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

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
	C17orf100	ENST00000634977.1	TSL:5	n.*324+3950G>A		intron	N/A	ENSP00000491769.1	A0A1W2PPW6
	C17orf100	ENST00000635042.1	TSL:5	n.*324+3950G>A		intron	N/A	ENSP00000491523.1	A8MU93

Frequencies

GnomAD3 genomes AF: 0.00391 AC: 565 AN: 144532 Hom.: 0 Cov.: 27

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000798 AC: 32 AN: 40110

American (AMR) AF: 0.0262 AC: 360 AN: 13754

Ashkenazi Jewish (ASJ) AF: 0.00510 AC: 16 AN: 3138

East Asian (EAS) AF: 0.000202 AC: 1 AN: 4942

South Asian (SAS) AF: 0.000871 AC: 4 AN: 4594

European-Finnish (FIN) AF: 0.000579 AC: 6 AN: 10356

Middle Eastern (MID) AF: 0.00355 AC: 1 AN: 282

European-Non Finnish (NFE) AF: 0.00207 AC: 134 AN: 64610

Other (OTH) AF: 0.00508 AC: 10 AN: 1970

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0113 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.90
PhyloP100		0.61

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: rs4796535;

hg19: chr17-6559863;