chr4-55908999-C-G

Variant names:

• chr4-55908999-C-G
• rs6833480
• ENST00000716477.1:n.304-18473G>C

Variant summary

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

The ENST00000716477.1(ENSG00000287382):​n.304-18473G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 151,932 control chromosomes in the GnomAD database, including 723 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 0.092 (723 hom., cov: 31)
• Consequence: ENSG00000287382 ENST00000716477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 3 publications found

Genes affected

ENSG00000287382 (HGNC:58376):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716477.1. 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
	ENSG00000287382	ENST00000716477.1		n.304-18473G>C		intron	N/A
	ENSG00000287382	ENST00000716478.1		n.389-6544G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0920 AC: 13973 AN: 151814 Hom.: 721 Cov.: 31

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0882

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

GnomAD4 genome AF: 0.0921 AC: 13986 AN: 151932 Hom.: 723 Cov.: 31 AF XY: 0.0897 AC XY: 6657 AN XY: 74236

African (AFR) AF: 0.0759 AC: 3147 AN: 41464

American (AMR) AF: 0.0999 AC: 1523 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5170

South Asian (SAS) AF: 0.0784 AC: 377 AN: 4808

European-Finnish (FIN) AF: 0.103 AC: 1088 AN: 10522

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7377 AN: 67944

Other (OTH) AF: 0.0868 AC: 183 AN: 2108

Alfa AF: 0.0479 Hom.: 45

Bravo AF: 0.0916

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6833480; hg19: chr4-56775165;