rs2040847

Positions:

• chr17-6654692-G-A

Variant summary

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

The ENST00000576138.1(ENSG00000261996):​n.119+199C>T 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 0.538 in 151,684 control chromosomes in the GnomAD database, including 22,219 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 0.54 (22219 hom., cov: 34)
• Consequence: ENST00000576138.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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
	ENST00000576138.1	n.119+199C>T		intron_variant, non_coding_transcript_variant		3
C17orf100	ENST00000634977.1	c.*324+2098G>A		intron_variant, NMD_transcript_variant		5
C17orf100	ENST00000635042.1	c.*324+2098G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81522 AN: 151566 Hom.: 22203 Cov.: 34

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.538 AC: 81573 AN: 151684 Hom.: 22219 Cov.: 34 AF XY: 0.538 AC XY: 39832 AN XY: 74094

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.523

Alfa AF: 0.514 Hom.: 3537

Bravo AF: 0.553

Asia WGS AF: 0.647 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040847; hg19: chr17-6558011;