4-87852697-T-G

Variant names:

• chr4-87852697-T-G
• rs6532023
• ENST00000829020.1:n.285+39556A>C

Variant summary

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

The ENST00000829020.1(ENSG00000307815):​n.285+39556A>C 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 152,056 control chromosomes in the GnomAD database, including 33,791 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 (33791 hom., cov: 33)
• Consequence: ENSG00000307815 ENST00000829020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 44 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307815	ENST00000829020.1		n.285+39556A>C		intron	N/A
	ENSG00000307815	ENST00000829021.1		n.340+39556A>C		intron	N/A
	ENSG00000307815	ENST00000829022.1		n.335+39556A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101206 AN: 151938 Hom.: 33760 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.666 AC: 101289 AN: 152056 Hom.: 33791 Cov.: 33 AF XY: 0.671 AC XY: 49876 AN XY: 74316

African (AFR) AF: 0.639 AC: 26491 AN: 41480

American (AMR) AF: 0.721 AC: 11012 AN: 15272

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

East Asian (EAS) AF: 0.670 AC: 3458 AN: 5160

South Asian (SAS) AF: 0.691 AC: 3329 AN: 4820

European-Finnish (FIN) AF: 0.699 AC: 7388 AN: 10568

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44900 AN: 67966

Other (OTH) AF: 0.656 AC: 1387 AN: 2114

Alfa AF: 0.664 Hom.: 88970

Bravo AF: 0.664

Asia WGS AF: 0.729 AC: 2529 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6532023;

hg19: chr4-88773849;