12-92593432-G-C

Variant names:

• chr12-92593432-G-C
• rs11829373
• XR_945211.3:n.315+35834G>C

Variant summary

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

The XR_945211.3(LOC105369905):​n.315+35834G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,136 control chromosomes in the GnomAD database, including 3,184 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 0.17 (3184 hom., cov: 32)
• Consequence: LOC105369905 XR_945211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 4 publications found

Genes affected

LOC105369905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.170 AC: 25811 AN: 152018 Hom.: 3172 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.170 AC: 25868 AN: 152136 Hom.: 3184 Cov.: 32 AF XY: 0.163 AC XY: 12133 AN XY: 74354

African (AFR) AF: 0.346 AC: 14365 AN: 41480

American (AMR) AF: 0.159 AC: 2432 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0877 AC: 304 AN: 3468

East Asian (EAS) AF: 0.0439 AC: 228 AN: 5190

South Asian (SAS) AF: 0.0667 AC: 321 AN: 4812

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6996 AN: 67980

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.0340 Hom.: 24

Bravo AF: 0.185

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.43
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs11829373; hg19: chr12-92987208;