XR_945388.3:n.118+13093C>T

Variant names:

• chr12-115749855-G-A
• rs2460488
• XR_945388.3:n.118+13093C>T

Variant summary

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

The XR_945388.3(LOC105370003):​n.118+13093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,114 control chromosomes in the GnomAD database, including 2,375 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 0.17 (2375 hom., cov: 32)
• Consequence: LOC105370003 XR_945388.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 5 publications found

Genes affected

LOC105370003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 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: 0.172 AC: 26168 AN: 151996 Hom.: 2368 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.172 AC: 26179 AN: 152114 Hom.: 2375 Cov.: 32 AF XY: 0.173 AC XY: 12884 AN XY: 74352

African (AFR) AF: 0.158 AC: 6545 AN: 41502

American (AMR) AF: 0.256 AC: 3907 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3472

East Asian (EAS) AF: 0.164 AC: 844 AN: 5150

South Asian (SAS) AF: 0.120 AC: 576 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1933 AN: 10572

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11112 AN: 67996

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.164 Hom.: 4041

Bravo AF: 0.178

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.82
DANN	Benign	0.61
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2460488; hg19: chr12-116187660;