rs6559058

Positions:

• chr8-5858345-A-G

Variant summary

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

The XR_941375.2(LOC105377795):​n.622T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,048 control chromosomes in the GnomAD database, including 4,161 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 0.21 (4161 hom., cov: 32)
• Consequence: LOC105377795 XR_941375.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

LOC105377795 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377795	XR_941375.2	n.622T>C		non_coding_transcript_exon_variant	6/6
LOC105377795	XR_941374.2	n.957T>C		non_coding_transcript_exon_variant	7/7

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31806 AN: 151930 Hom.: 4166 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.209 AC: 31797 AN: 152048 Hom.: 4161 Cov.: 32 AF XY: 0.207 AC XY: 15387 AN XY: 74298

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0198

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.225

Alfa AF: 0.238 Hom.: 1181

Bravo AF: 0.200

Asia WGS AF: 0.0910 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6559058; hg19: chr8-5715867;