rs10492336

Variant names:

• chr12-114147775-A-C
• rs10492336
• ENST00000552413.2:n.1108-14453A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-114147775-A-C
• chr12-114147775-A-T

Variant summary

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

The ENST00000552413.2(ENSG00000257997):​n.1108-14453A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,198 control chromosomes in the GnomAD database, including 45,533 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 0.76 (45533 hom., cov: 32)
• Consequence: ENSG00000257997 ENST00000552413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 11 publications found

Genes affected

ENSG00000257997 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552413.2. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000257997	ENST00000552413.2	TSL:4	n.1108-14453A>C		intron	N/A
	ENSG00000257997	ENST00000777255.1		n.457-47318A>C		intron	N/A
	ENSG00000257997	ENST00000777256.1		n.449-30985A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116275 AN: 152080 Hom.: 45484 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.765 AC: 116385 AN: 152198 Hom.: 45533 Cov.: 32 AF XY: 0.766 AC XY: 56982 AN XY: 74400

African (AFR) AF: 0.931 AC: 38677 AN: 41556

American (AMR) AF: 0.802 AC: 12267 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4188 AN: 5174

South Asian (SAS) AF: 0.790 AC: 3809 AN: 4824

European-Finnish (FIN) AF: 0.676 AC: 7157 AN: 10586

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45481 AN: 67976

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.695 Hom.: 49444

Bravo AF: 0.781

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.46
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10492336; hg19: chr12-114585580;