XR_929046.3:n.2682A>G

Variant names:

• chr8-73234531-A-G
• rs2605877
• XR_929046.3:n.2682A>G

Variant summary

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

The XR_929046.3(LOC105375901):​n.2682A>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 0.688 in 151,950 control chromosomes in the GnomAD database, including 36,095 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 0.69 (36095 hom., cov: 31)
• Consequence: LOC105375901 XR_929046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 6 publications found

Genes affected

LOC105375901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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: 0.688 AC: 104525 AN: 151832 Hom.: 36068 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.688 AC: 104595 AN: 151950 Hom.: 36095 Cov.: 31 AF XY: 0.688 AC XY: 51065 AN XY: 74242

African (AFR) AF: 0.652 AC: 26996 AN: 41384

American (AMR) AF: 0.720 AC: 10990 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2268 AN: 3464

East Asian (EAS) AF: 0.792 AC: 4082 AN: 5154

South Asian (SAS) AF: 0.729 AC: 3510 AN: 4818

European-Finnish (FIN) AF: 0.696 AC: 7353 AN: 10558

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47111 AN: 67996

Other (OTH) AF: 0.683 AC: 1440 AN: 2108

Alfa AF: 0.691 Hom.: 67450

Bravo AF: 0.688

Asia WGS AF: 0.725 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.59
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2605877; hg19: chr8-74146766;