ENST00000805146.1:n.496+4073C>T

Variant names:

• chr3-28165386-G-A
• rs9310862
• ENST00000805146.1:n.496+4073C>T

Variant summary

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

The ENST00000805146.1(ENSG00000304655):​n.496+4073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,000 control chromosomes in the GnomAD database, including 17,825 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 0.48 (17825 hom., cov: 32)
• Consequence: ENSG00000304655 ENST00000805146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 0 publications found

Genes affected

ENSG00000304655 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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
ENSG00000304655	ENST00000805146.1	n.496+4073C>T		intron_variant	Intron 2 of 4
ENSG00000304655	ENST00000805147.1	n.499+4073C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73340 AN: 151882 Hom.: 17817 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.483 AC: 73384 AN: 152000 Hom.: 17825 Cov.: 32 AF XY: 0.482 AC XY: 35840 AN XY: 74296

African (AFR) AF: 0.437 AC: 18095 AN: 41450

American (AMR) AF: 0.483 AC: 7371 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3062 AN: 5150

South Asian (SAS) AF: 0.571 AC: 2749 AN: 4818

European-Finnish (FIN) AF: 0.448 AC: 4735 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33873 AN: 67976

Other (OTH) AF: 0.521 AC: 1099 AN: 2110

Alfa AF: 0.491 Hom.: 15485

Bravo AF: 0.487

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.085
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9310862; hg19: chr3-28206877;