rs2046211

Positions:

• chr6-151627149-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.575C>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0228

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.00830

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0232

Gnomad4 OTH AF: 0.0355

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046211; hg19: chr6-151948284;