chr17-63919116-C-A

Variant names:

• chr17-63919116-C-A
• rs2005171
• ENST00000647774.1:c.287-610G>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000647774.1(ENSG00000285947):​c.287-610G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,134 control chromosomes in the GnomAD database, including 9,849 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (9849 hom., cov: 33)
• Consequence: ENSG00000285947 ENST00000647774.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0410
• Publications: 8 publications found

Genes affected

ENSG00000285947 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 17-63919116-C-A is Benign according to our data. Variant chr17-63919116-C-A is described in ClinVar as Benign. ClinVar VariationId is 1296534.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647774.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285947	ENST00000647774.1		c.287-610G>T		intron	N/A	ENSP00000497443.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52269 AN: 152018 Hom.: 9841 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.344 AC: 52300 AN: 152134 Hom.: 9849 Cov.: 33 AF XY: 0.341 AC XY: 25364 AN XY: 74368

African (AFR) AF: 0.186 AC: 7707 AN: 41510

American (AMR) AF: 0.352 AC: 5387 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5168

South Asian (SAS) AF: 0.282 AC: 1362 AN: 4822

European-Finnish (FIN) AF: 0.395 AC: 4179 AN: 10584

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28707 AN: 67982

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.242 Hom.: 609

Bravo AF: 0.338

Asia WGS AF: 0.332 AC: 1157 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 12655556)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		-0.041
PromoterAI		0.043	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2005171; hg19: chr17-61996476;