4-69050923-GA-G

Variant names:

• chr4-69050923-GA-G
• rs5859158
• ENST00000766642.1:n.52-3805delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000766642.1(ENSG00000299813):​n.52-3805delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,052 control chromosomes in the GnomAD database, including 3,243 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3243 hom., cov: 28)
• Consequence: ENSG00000299813 ENST00000766642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 1 publications found

Genes affected

ENSG00000299813 (HGNC:58801):

LOC105377265 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766642.1. 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
	ENSG00000299813	ENST00000766642.1		n.52-3805delT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30598 AN: 151934 Hom.: 3242 Cov.: 28

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30615 AN: 152052 Hom.: 3243 Cov.: 28 AF XY: 0.201 AC XY: 14931 AN XY: 74330

African (AFR) AF: 0.253 AC: 10491 AN: 41464

American (AMR) AF: 0.166 AC: 2541 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3470

East Asian (EAS) AF: 0.175 AC: 903 AN: 5164

South Asian (SAS) AF: 0.224 AC: 1077 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2168 AN: 10576

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.177 AC: 12023 AN: 67986

Other (OTH) AF: 0.197 AC: 416 AN: 2108

Alfa AF: 0.180 Hom.: 328

Bravo AF: 0.197

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.085

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs5859158; hg19: chr4-69916641;