XR_001745931.2:n.752+289G>T

Variant names:

• chr8-63308096-G-T
• rs7837234
• XR_001745931.2:n.752+289G>T

Variant summary

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

The XR_001745931.2(LOC105375873):​n.752+289G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,898 control chromosomes in the GnomAD database, including 9,428 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 0.35 (9428 hom., cov: 31)
• Consequence: LOC105375873 XR_001745931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 5 publications found

Genes affected

LOC105375873 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52470 AN: 151780 Hom.: 9409 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.346 AC: 52536 AN: 151898 Hom.: 9428 Cov.: 31 AF XY: 0.341 AC XY: 25311 AN XY: 74228

African (AFR) AF: 0.355 AC: 14716 AN: 41412

American (AMR) AF: 0.334 AC: 5084 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3460

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5170

South Asian (SAS) AF: 0.364 AC: 1749 AN: 4802

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10544

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25250 AN: 67952

Other (OTH) AF: 0.369 AC: 778 AN: 2108

Alfa AF: 0.364 Hom.: 43453

Bravo AF: 0.346

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7837234; hg19: chr8-64220654;