XR_001749129.2:n.2897C>T

Variant names:

• chr12-49946258-C-T
• rs7314734
• XR_001749129.2:n.2897C>T

Variant summary

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

The XR_001749129.2(LOC105369763):​n.2897C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0936 in 152,170 control chromosomes in the GnomAD database, including 1,336 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 0.094 (1336 hom., cov: 33)
• Consequence: LOC105369763 XR_001749129.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 4 publications found

Genes affected

LOC105369763 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.0935 AC: 14214 AN: 152052 Hom.: 1326 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0936 AC: 14246 AN: 152170 Hom.: 1336 Cov.: 33 AF XY: 0.0950 AC XY: 7068 AN XY: 74394

African (AFR) AF: 0.205 AC: 8504 AN: 41486

American (AMR) AF: 0.192 AC: 2934 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.0922 AC: 478 AN: 5182

South Asian (SAS) AF: 0.153 AC: 736 AN: 4824

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1160 AN: 68022

Other (OTH) AF: 0.0800 AC: 169 AN: 2112

Alfa AF: 0.0475 Hom.: 887

Bravo AF: 0.109

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.70
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7314734; hg19: chr12-50340041;