XR_007059816.1:n.575C>G

Variant names:

• chr6-151627149-C-G
• rs2046211
• XR_007059816.1:n.575C>G

Variant summary

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

The XR_007059816.1(LOC124901435):​n.575C>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 0.0456 in 152,260 control chromosomes in the GnomAD database, including 267 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 0.046 (267 hom., cov: 32)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 9 publications found

Genes affected

LOC124901435 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6926 AN: 152142 Hom.: 266 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.00850

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0456 AC: 6938 AN: 152260 Hom.: 267 Cov.: 32 AF XY: 0.0444 AC XY: 3305 AN XY: 74440

African (AFR) AF: 0.108 AC: 4498 AN: 41530

American (AMR) AF: 0.0228 AC: 349 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3466

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5180

South Asian (SAS) AF: 0.00830 AC: 40 AN: 4820

European-Finnish (FIN) AF: 0.0188 AC: 200 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0232 AC: 1577 AN: 68024

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0366 Hom.: 26

Bravo AF: 0.0498

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.42
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2046211; hg19: chr6-151948284;