chr4-87854091-T-C

Variant names:

• chr4-87854091-T-C
• rs1471403
• ENST00000829020.1:n.285+38162A>G

Variant summary

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

The ENST00000829020.1(ENSG00000307815):​n.285+38162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,050 control chromosomes in the GnomAD database, including 33,826 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 (33826 hom., cov: 32)
• Consequence: ENSG00000307815 ENST00000829020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 47 publications found

Genes affected

ENSG00000307815 (HGNC:58843):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 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
ENSG00000307815	ENST00000829020.1	n.285+38162A>G		intron_variant	Intron 3 of 5
ENSG00000307815	ENST00000829021.1	n.340+38162A>G		intron_variant	Intron 3 of 4
ENSG00000307815	ENST00000829022.1	n.335+38162A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101250 AN: 151930 Hom.: 33795 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.666 AC: 101334 AN: 152050 Hom.: 33826 Cov.: 32 AF XY: 0.671 AC XY: 49907 AN XY: 74326

African (AFR) AF: 0.639 AC: 26492 AN: 41456

American (AMR) AF: 0.721 AC: 11031 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2404 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3454 AN: 5164

South Asian (SAS) AF: 0.691 AC: 3325 AN: 4810

European-Finnish (FIN) AF: 0.700 AC: 7407 AN: 10578

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44916 AN: 67960

Other (OTH) AF: 0.657 AC: 1386 AN: 2110

Alfa AF: 0.663 Hom.: 69459

Bravo AF: 0.665

Asia WGS AF: 0.730 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1471403; hg19: chr4-88775243;