chr6-166042608-G-A

Position:

• chr6-166042608-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105378117 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378117	XR_943241.2	n.522G>A		non_coding_transcript_exon_variant	4/4

Ensembl

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

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

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.810

Alfa AF: 0.815 Hom.: 40801

Bravo AF: 0.808

Asia WGS AF: 0.954 AC: 3317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs777574; hg19: chr6-166456096;