8-73234531-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375901	XR_929046.3	n.2682A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;