ENST00000759721.1:n.90+4908T>C

Variant names:

• chr3-108820344-A-G
• rs10933964
• ENST00000759721.1:n.90+4908T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000759721.1(ENSG00000298997):​n.90+4908T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,178 control chromosomes in the GnomAD database, including 12,839 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 0.39 (12839 hom., cov: 31)
• Consequence: ENSG00000298997 ENST00000759721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 2 publications found

Genes affected

ENSG00000298997 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759721.1. 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
	ENSG00000298997	ENST00000759721.1		n.90+4908T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58688 AN: 151058 Hom.: 12833 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.388 AC: 58692 AN: 151178 Hom.: 12839 Cov.: 31 AF XY: 0.387 AC XY: 28539 AN XY: 73776

African (AFR) AF: 0.188 AC: 7771 AN: 41328

American (AMR) AF: 0.416 AC: 6266 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1716 AN: 3460

East Asian (EAS) AF: 0.136 AC: 681 AN: 5016

South Asian (SAS) AF: 0.373 AC: 1765 AN: 4730

European-Finnish (FIN) AF: 0.512 AC: 5362 AN: 10474

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.499 AC: 33836 AN: 67804

Other (OTH) AF: 0.395 AC: 831 AN: 2104

Alfa AF: 0.425 Hom.: 2178

Bravo AF: 0.369

Asia WGS AF: 0.243 AC: 850 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.87
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs10933964; hg19: chr3-108539191;