17-47993340-A-G

Variant names:

• chr17-47993340-A-G
• rs2597165
• ENST00000578239.2:n.246+2611T>C

Variant summary

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

The ENST00000578239.2(ENSG00000264701):​n.246+2611T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,008 control chromosomes in the GnomAD database, including 34,859 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 0.67 (34859 hom., cov: 31)
• Consequence: ENSG00000264701 ENST00000578239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 5 publications found

Genes affected

ENSG00000264701 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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
ENSG00000264701	ENST00000578239.2	n.246+2611T>C		intron_variant	Intron 1 of 1	4
ENSG00000264701	ENST00000732413.1	n.71-12658T>C		intron_variant	Intron 1 of 1
ENSG00000264701	ENST00000732414.1	n.331+2611T>C		intron_variant	Intron 3 of 3
ENSG00000289599	ENST00000732594.1	n.238+10609A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101673 AN: 151890 Hom.: 34836 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.669 AC: 101746 AN: 152008 Hom.: 34859 Cov.: 31 AF XY: 0.670 AC XY: 49761 AN XY: 74294

African (AFR) AF: 0.521 AC: 21590 AN: 41436

American (AMR) AF: 0.638 AC: 9740 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2343 AN: 3472

East Asian (EAS) AF: 0.757 AC: 3893 AN: 5146

South Asian (SAS) AF: 0.687 AC: 3304 AN: 4810

European-Finnish (FIN) AF: 0.796 AC: 8421 AN: 10582

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50062 AN: 67984

Other (OTH) AF: 0.698 AC: 1472 AN: 2108

Alfa AF: 0.717 Hom.: 18340

Bravo AF: 0.652

Asia WGS AF: 0.659 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	17
DANN	Benign	0.42
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2597165; hg19: chr17-46070706;