17-47713757-T-G

Variant names:

• chr17-47713757-T-G
• rs2013383
• ENST00000768833.1:n.327+4937A>C

Variant summary

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

The ENST00000768833.1(ENSG00000300104):​n.327+4937A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,000 control chromosomes in the GnomAD database, including 29,916 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 0.62 (29916 hom., cov: 32)
• Consequence: ENSG00000300104 ENST00000768833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 7 publications found

Genes affected

ENSG00000300104 (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 = 0.726 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
ENSG00000300104	ENST00000768833.1	n.327+4937A>C		intron_variant	Intron 2 of 2
ENSG00000300104	ENST00000768834.1	n.164+4937A>C		intron_variant	Intron 1 of 1
ENSG00000300104	ENST00000768835.1	n.391-1086A>C		intron_variant	Intron 3 of 3
ENSG00000300104	ENST00000768836.1	n.135-1086A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94277 AN: 151882 Hom.: 29866 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.621 AC: 94373 AN: 152000 Hom.: 29916 Cov.: 32 AF XY: 0.615 AC XY: 45696 AN XY: 74288

African (AFR) AF: 0.733 AC: 30378 AN: 41452

American (AMR) AF: 0.537 AC: 8211 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2289 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3165 AN: 5160

South Asian (SAS) AF: 0.565 AC: 2720 AN: 4812

European-Finnish (FIN) AF: 0.513 AC: 5428 AN: 10580

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40147 AN: 67932

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.512 Hom.: 1882

Bravo AF: 0.627

Asia WGS AF: 0.512 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.34
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs2013383; hg19: chr17-45791123;