chr17-5739998-C-A

Variant names:

• chr17-5739998-C-A
• rs8080616
• ENST00000783338.1:n.186+32672G>T

Variant summary

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

The ENST00000783338.1(ENSG00000286356):​n.186+32672G>T 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 0.0021 (8 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000286356 ENST00000783338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

ENSG00000286356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783338.1. 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
	ENSG00000286356	ENST00000783338.1		n.186+32672G>T		intron	N/A
	ENSG00000286356	ENST00000783339.1		n.174-20653G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00215 AC: 310 AN: 144374 Hom.: 8 Cov.: 27

Gnomad AFR AF: 0.000491

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000615

Gnomad ASJ AF: 0.00674

Gnomad EAS AF: 0.000843

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.000914

Gnomad MID AF: 0.0166

Gnomad NFE AF: 0.00154

Gnomad OTH AF: 0.00297

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: 0.00213 AC: 308 AN: 144446 Hom.: 8 Cov.: 27 AF XY: 0.00259 AC XY: 181 AN XY: 69952

African (AFR) AF: 0.000490 AC: 19 AN: 38796

American (AMR) AF: 0.000615 AC: 9 AN: 14640

Ashkenazi Jewish (ASJ) AF: 0.00674 AC: 23 AN: 3412

East Asian (EAS) AF: 0.000846 AC: 4 AN: 4728

South Asian (SAS) AF: 0.0294 AC: 133 AN: 4518

European-Finnish (FIN) AF: 0.000914 AC: 8 AN: 8754

Middle Eastern (MID) AF: 0.0180 AC: 5 AN: 278

European-Non Finnish (NFE) AF: 0.00152 AC: 101 AN: 66406

Other (OTH) AF: 0.00294 AC: 6 AN: 2042

Alfa AF: 0.00335 Hom.: 634

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs8080616; hg19: chr17-5643318;