chr4-87878558-T-C

Variant names:

• chr4-87878558-T-C
• rs1463104
• ENST00000829020.1:n.285+13695A>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+13695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,988 control chromosomes in the GnomAD database, including 7,907 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 0.32 (7907 hom., cov: 32)
• Consequence: ENSG00000307815 ENST00000829020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 22 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829020.1. 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
	ENSG00000307815	ENST00000829020.1		n.285+13695A>G		intron	N/A
	ENSG00000307815	ENST00000829021.1		n.340+13695A>G		intron	N/A
	ENSG00000307815	ENST00000829022.1		n.335+13695A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48656 AN: 151870 Hom.: 7901 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.320 AC: 48694 AN: 151988 Hom.: 7907 Cov.: 32 AF XY: 0.315 AC XY: 23417 AN XY: 74294

African (AFR) AF: 0.286 AC: 11843 AN: 41448

American (AMR) AF: 0.323 AC: 4934 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1429 AN: 5186

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4818

European-Finnish (FIN) AF: 0.345 AC: 3639 AN: 10534

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23566 AN: 67952

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.338 Hom.: 26568

Bravo AF: 0.322

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.87
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1463104; hg19: chr4-88799710;