rs5859158

Variant names:

• chr4-69050923-GA-G
• rs5859158
• XR_001741714.2:n.3048-788delT

Your query was ambiguous. Multiple possible variants found:

• chr4-69050923-GA-G
• chr4-69050923-GA-GAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_938851.2(LOC105377265):​n.316-788delT 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: LOC105377265 XR_938851.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

LOC105377265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377265	XR_001741714.2	n.3048-788delT		intron_variant	Intron 2 of 4
LOC105377265	XR_938851.2	n.316-788delT		intron_variant	Intron 1 of 3
LOC105377265	XR_938852.2	n.316-896delT		intron_variant	Intron 1 of 3
LOC105377265	XR_938854.2	n.298-788delT		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.197

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 v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs5859158; hg19: chr4-69916641;