rs6559058

Variant names:

• chr8-5858345-A-G
• rs6559058
• ENST00000747096.1:n.581T>C

Variant summary

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

The ENST00000747096.1(ENSG00000297321):​n.581T>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: ENSG00000297321 ENST00000747096.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 2 publications found

Genes affected

ENSG00000297321 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105377795	XR_941374.2	n.957T>C		non_coding_transcript_exon_variant	Exon 7 of 7
LOC105377795	XR_941375.2	n.622T>C		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297321	ENST00000747096.1	n.581T>C		non_coding_transcript_exon_variant	Exon 6 of 6
ENSG00000297321	ENST00000747097.1	n.483T>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000297321	ENST00000747098.1	n.504T>C		non_coding_transcript_exon_variant	Exon 5 of 5

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

African (AFR) AF: 0.0670 AC: 2780 AN: 41522

American (AMR) AF: 0.235 AC: 3586 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3466

East Asian (EAS) AF: 0.0198 AC: 102 AN: 5162

South Asian (SAS) AF: 0.154 AC: 741 AN: 4818

European-Finnish (FIN) AF: 0.319 AC: 3360 AN: 10548

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19770 AN: 67958

Other (OTH) AF: 0.225 AC: 474 AN: 2108

Alfa AF: 0.229 Hom.: 1935

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
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs6559058; hg19: chr8-5715867;