chr17-6020788-G-A

Variant names:

• chr17-6020788-G-A
• rs6502901
• ENST00000573619.1:c.-289+30767G>A

Variant summary

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

The ENST00000573619.1(ENSG00000285471):​c.-289+30767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,164 control chromosomes in the GnomAD database, including 9,049 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 0.31 (9049 hom., cov: 33)
• Consequence: ENSG00000285471 ENST00000573619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 2 publications found

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573619.1. 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
	ENSG00000285471	ENST00000573619.1	TSL:2	c.-289+30767G>A		intron	N/A	ENSP00000461865.1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47875 AN: 152046 Hom.: 9051 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.315 AC: 47877 AN: 152164 Hom.: 9049 Cov.: 33 AF XY: 0.307 AC XY: 22817 AN XY: 74412

African (AFR) AF: 0.145 AC: 6038 AN: 41534

American (AMR) AF: 0.371 AC: 5677 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3470

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5182

South Asian (SAS) AF: 0.148 AC: 712 AN: 4822

European-Finnish (FIN) AF: 0.342 AC: 3616 AN: 10580

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29452 AN: 67970

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.400 Hom.: 35614

Bravo AF: 0.313

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6502901; hg19: chr17-5924108; COSMIC: COSV73818517;