12-67683408-A-G

Variant names:

• chr12-67683408-A-G
• rs6581768
• XR_945051.3:n.10230A>G

Variant summary

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

The XR_945051.3(LOC105369816):​n.10230A>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 0.252 in 152,096 control chromosomes in the GnomAD database, including 5,377 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 0.25 (5377 hom., cov: 32)
• Consequence: LOC105369816 XR_945051.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 publications found

Genes affected

LOC105369816 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 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: 0.252 AC: 38366 AN: 151978 Hom.: 5379 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.252 AC: 38356 AN: 152096 Hom.: 5377 Cov.: 32 AF XY: 0.251 AC XY: 18676 AN XY: 74344

African (AFR) AF: 0.122 AC: 5069 AN: 41522

American (AMR) AF: 0.300 AC: 4582 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1809 AN: 5160

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4812

European-Finnish (FIN) AF: 0.196 AC: 2072 AN: 10584

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21007 AN: 67954

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.265 Hom.: 699

Bravo AF: 0.254

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.76
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6581768; hg19: chr12-68077188; COSMIC: COSV51093992;