8-117310212-A-G

Variant names:

• chr8-117310212-A-G
• rs12155554
• XR_928573.3:n.469A>G

Variant summary

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

The XR_928573.3(LOC105375717):​n.469A>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 0.052 in 152,064 control chromosomes in the GnomAD database, including 312 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 0.052 (312 hom., cov: 32)
• Consequence: LOC105375717 XR_928573.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 2 publications found

Genes affected

LOC105375717 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671266.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286308	ENST00000671266.1		n.47-5486A>G		intron	N/A
	ENSG00000286308	ENST00000754617.1		n.194-5486A>G		intron	N/A
	ENSG00000286308	ENST00000754618.1		n.194-5486A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7886 AN: 151946 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0246

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0520 AC: 7905 AN: 152064 Hom.: 312 Cov.: 32 AF XY: 0.0568 AC XY: 4222 AN XY: 74338

African (AFR) AF: 0.0464 AC: 1926 AN: 41486

American (AMR) AF: 0.0293 AC: 447 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3472

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5184

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4812

European-Finnish (FIN) AF: 0.0726 AC: 767 AN: 10564

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2994 AN: 67976

Other (OTH) AF: 0.0579 AC: 122 AN: 2106

Alfa AF: 0.0451 Hom.: 52

Bravo AF: 0.0435

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0030
DANN	Benign	0.31
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs12155554; hg19: chr8-118322451;