rs6833480

Positions:

• chr4-55908999-C-G
• chr4-55908999-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058123.1(LOC105377663):​n.290-18473G>C variant causes a intron, non coding transcript 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: LOC105377663 XR_007058123.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

LOC105377663 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377663	XR_007058123.1	n.290-18473G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0759

Gnomad4 AMR AF: 0.0999

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0784

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0868

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6833480; hg19: chr4-56775165;