3-115350302-T-G

Variant names:

• chr3-115350302-T-G
• rs10514758
• ENST00000653398.1:n.777-19757T>G

Variant summary

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

The ENST00000653398.1(ENSG00000242880):​n.777-19757T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,032 control chromosomes in the GnomAD database, including 2,124 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 0.11 (2124 hom., cov: 32)
• Consequence: ENSG00000242880 ENST00000653398.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 1 publications found

Genes affected

ENSG00000242880 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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
ENSG00000242880	ENST00000653398.1	n.777-19757T>G		intron_variant	Intron 6 of 6
ENSG00000242880	ENST00000656753.1	n.698-19757T>G		intron_variant	Intron 6 of 6
ENSG00000242880	ENST00000657371.1	n.592+87372T>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17021 AN: 151916 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0857

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

GnomAD4 genome AF: 0.112 AC: 17060 AN: 152032 Hom.: 2124 Cov.: 32 AF XY: 0.110 AC XY: 8166 AN XY: 74344

African (AFR) AF: 0.311 AC: 12915 AN: 41476

American (AMR) AF: 0.0645 AC: 983 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3468

East Asian (EAS) AF: 0.0504 AC: 260 AN: 5158

South Asian (SAS) AF: 0.0754 AC: 364 AN: 4828

European-Finnish (FIN) AF: 0.0320 AC: 340 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1956 AN: 67940

Other (OTH) AF: 0.0848 AC: 179 AN: 2110

Alfa AF: 0.0474 Hom.: 117

Bravo AF: 0.124

Asia WGS AF: 0.0900 AC: 315 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.40
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10514758; hg19: chr3-115069149;