chr12-84492794-T-G

Variant names:

• chr12-84492794-T-G
• rs993226
• XR_945151.2:n.333A>C

Variant summary

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

The XR_945151.2(LOC105369875):​n.333A>C 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 0.0612 in 152,140 control chromosomes in the GnomAD database, including 432 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 0.061 (432 hom., cov: 32)
• Consequence: LOC105369875 XR_945151.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878
• Publications: 7 publications found

Genes affected

LOC105369875 (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 (AFR) allele frequency at 95% confidence interval = 0.128 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: 0.0612 AC: 9297 AN: 152022 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0161

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0612 AC: 9307 AN: 152140 Hom.: 432 Cov.: 32 AF XY: 0.0575 AC XY: 4276 AN XY: 74376

African (AFR) AF: 0.131 AC: 5449 AN: 41522

American (AMR) AF: 0.0385 AC: 588 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0355 AC: 123 AN: 3466

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5140

South Asian (SAS) AF: 0.0159 AC: 77 AN: 4830

European-Finnish (FIN) AF: 0.0333 AC: 354 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0375 AC: 2550 AN: 67962

Other (OTH) AF: 0.0581 AC: 123 AN: 2116

Alfa AF: 0.0407 Hom.: 332

Bravo AF: 0.0660

Asia WGS AF: 0.0160 AC: 56 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	7.5
DANN	Benign	0.75
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs993226; hg19: chr12-84886573;