6-166042608-G-A

Variant names:

• chr6-166042608-G-A
• rs777574
• XR_943241.2:n.522G>A

Variant summary

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

The XR_943241.2(LOC105378117):​n.522G>A 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 0.811 in 152,108 control chromosomes in the GnomAD database, including 50,186 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 0.81 (50186 hom., cov: 31)
• Consequence: LOC105378117 XR_943241.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 publications found

Genes affected

LOC105378117 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.811 AC: 123249 AN: 151990 Hom.: 50135 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.811 AC: 123355 AN: 152108 Hom.: 50186 Cov.: 31 AF XY: 0.816 AC XY: 60692 AN XY: 74362

African (AFR) AF: 0.762 AC: 31608 AN: 41482

American (AMR) AF: 0.860 AC: 13134 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2715 AN: 3468

East Asian (EAS) AF: 0.979 AC: 5057 AN: 5168

South Asian (SAS) AF: 0.950 AC: 4575 AN: 4814

European-Finnish (FIN) AF: 0.832 AC: 8800 AN: 10576

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54736 AN: 68008

Other (OTH) AF: 0.810 AC: 1707 AN: 2108

Alfa AF: 0.809 Hom.: 119210

Bravo AF: 0.808

Asia WGS AF: 0.954 AC: 3317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs777574; hg19: chr6-166456096;