rs12545109

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-56401347-A-C
• chr8-56401347-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375849	XR_928910.2	n.521-3605T>G		intron_variant	Intron 5 of 6

Ensembl

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

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 v4.3

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;