17-6654692-G-A

Variant names:

• chr17-6654692-G-A
• rs2040847
• ENST00000576138.1:n.119+199C>T

Variant summary

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

The ENST00000576138.1(ENSG00000261996):​n.119+199C>T variant causes a intron 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: ENSG00000261996 ENST00000576138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 10 publications found

Genes affected

ENSG00000261996 (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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261996	ENST00000576138.1	n.119+199C>T		intron_variant	Intron 1 of 1	3
C17orf100	ENST00000634977.1	n.*324+2098G>A		intron_variant	Intron 1 of 1	5		ENSP00000491769.1
C17orf100	ENST00000635042.1	n.*324+2098G>A		intron_variant	Intron 1 of 1	5		ENSP00000491523.1

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

African (AFR) AF: 0.614 AC: 25355 AN: 41274

American (AMR) AF: 0.573 AC: 8743 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3638 AN: 5138

South Asian (SAS) AF: 0.576 AC: 2777 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4615 AN: 10538

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33114 AN: 67880

Other (OTH) AF: 0.523 AC: 1105 AN: 2112

Alfa AF: 0.514 Hom.: 27475

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2040847; hg19: chr17-6558011;