rs10131267

Variant names:

• chr14-30399530-G-A
• rs10131267
• XR_007064106.1:n.1275+12641C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-30399530-G-A
• chr14-30399530-G-C

Variant summary

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

The XR_007064106.1(LOC112267868):​n.1275+12641C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 152,108 control chromosomes in the GnomAD database, including 816 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 0.098 (816 hom., cov: 32)
• Consequence: LOC112267868 XR_007064106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

LOC112267868 (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 (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14893 AN: 151990 Hom.: 814 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0980 AC: 14908 AN: 152108 Hom.: 816 Cov.: 32 AF XY: 0.0984 AC XY: 7318 AN XY: 74364

African (AFR) AF: 0.134 AC: 5544 AN: 41476

American (AMR) AF: 0.0861 AC: 1317 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3470

East Asian (EAS) AF: 0.0331 AC: 171 AN: 5168

South Asian (SAS) AF: 0.150 AC: 724 AN: 4812

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5486 AN: 67988

Other (OTH) AF: 0.108 AC: 228 AN: 2102

Alfa AF: 0.0488 Hom.: 39

Bravo AF: 0.0948

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.36
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10131267; hg19: chr14-30868736;