XR_002957396.2:n.129T>G

Variant names:

• chr12-6345932-T-G
• rs11064145
• XR_002957396.2:n.129T>G

Variant summary

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

The XR_002957396.2(LOC112268088):​n.129T>G 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 0.486 in 152,060 control chromosomes in the GnomAD database, including 18,548 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 0.49 (18548 hom., cov: 32)
• Consequence: LOC112268088 XR_002957396.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 20 publications found

Genes affected

LOC112268088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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: 0.486 AC: 73884 AN: 151942 Hom.: 18545 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.486 AC: 73922 AN: 152060 Hom.: 18548 Cov.: 32 AF XY: 0.485 AC XY: 36037 AN XY: 74332

African (AFR) AF: 0.601 AC: 24924 AN: 41472

American (AMR) AF: 0.474 AC: 7243 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1185 AN: 5164

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4820

European-Finnish (FIN) AF: 0.463 AC: 4895 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30606 AN: 67960

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.453 Hom.: 18739

Bravo AF: 0.488

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.72
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs11064145; hg19: chr12-6455098;