17-62875908-G-A

Variant names:

• chr17-62875908-G-A
• rs2109265
• ENST00000847560.1:n.323+589G>A

Variant summary

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

The ENST00000847560.1(ENSG00000310142):​n.323+589G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,006 control chromosomes in the GnomAD database, including 24,965 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 (24965 hom., cov: 31)
• Consequence: ENSG00000310142 ENST00000847560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 6 publications found

Genes affected

ENSG00000310142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847560.1. 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
	ENSG00000310142	ENST00000847560.1		n.323+589G>A		intron	N/A
	ENSG00000310142	ENST00000847561.1		n.131+589G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81468 AN: 151888 Hom.: 24905 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.537 AC: 81584 AN: 152006 Hom.: 24965 Cov.: 31 AF XY: 0.529 AC XY: 39330 AN XY: 74290

African (AFR) AF: 0.849 AC: 35224 AN: 41478

American (AMR) AF: 0.390 AC: 5957 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1525 AN: 3462

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5170

South Asian (SAS) AF: 0.432 AC: 2078 AN: 4814

European-Finnish (FIN) AF: 0.447 AC: 4714 AN: 10542

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29273 AN: 67948

Other (OTH) AF: 0.490 AC: 1035 AN: 2112

Alfa AF: 0.453 Hom.: 70565

Bravo AF: 0.544

Asia WGS AF: 0.420 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.27
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2109265; hg19: chr17-60953269;