6-90498823-T-C

Variant names:

• chr6-90498823-T-C
• rs284511
• XR_007059678.1:n.2458A>G

Variant summary

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

The XR_007059678.1(LOC124901362):​n.2458A>G 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 0.555 in 151,448 control chromosomes in the GnomAD database, including 24,491 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 0.55 (24491 hom., cov: 32)
• Consequence: LOC124901362 XR_007059678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 6 publications found

Genes affected

LOC124901362 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83879 AN: 151328 Hom.: 24443 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.555 AC: 83981 AN: 151448 Hom.: 24491 Cov.: 32 AF XY: 0.546 AC XY: 40415 AN XY: 74016

African (AFR) AF: 0.729 AC: 30227 AN: 41448

American (AMR) AF: 0.404 AC: 6137 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2369 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1602 AN: 4988

South Asian (SAS) AF: 0.564 AC: 2678 AN: 4748

European-Finnish (FIN) AF: 0.399 AC: 4169 AN: 10448

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34934 AN: 67858

Other (OTH) AF: 0.573 AC: 1210 AN: 2110

Alfa AF: 0.328 Hom.: 742

Bravo AF: 0.550

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.88
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs284511; hg19: chr6-91208542;