chr8-56401347-A-C

Variant names:

• chr8-56401347-A-C
• rs12545109
• XR_928910.2:n.521-3605T>G

Variant summary

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

The XR_928910.2(LOC105375849):​n.521-3605T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,100 control chromosomes in the GnomAD database, including 40,295 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 0.72 (40295 hom., cov: 32)
• Consequence: LOC105375849 XR_928910.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 20 publications found

Genes affected

LOC105375849 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.778 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: 0.725 AC: 110158 AN: 151982 Hom.: 40270 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.725 AC: 110233 AN: 152100 Hom.: 40295 Cov.: 32 AF XY: 0.725 AC XY: 53906 AN XY: 74352

African (AFR) AF: 0.636 AC: 26367 AN: 41462

American (AMR) AF: 0.735 AC: 11237 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3512 AN: 5170

South Asian (SAS) AF: 0.799 AC: 3856 AN: 4824

European-Finnish (FIN) AF: 0.800 AC: 8468 AN: 10590

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51596 AN: 67994

Other (OTH) AF: 0.727 AC: 1531 AN: 2106

Alfa AF: 0.746 Hom.: 182043

Bravo AF: 0.714

Asia WGS AF: 0.775 AC: 2696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12545109; hg19: chr8-57313906;