rs1794899

Variant names:

• chr12-121105170-A-G
• rs1794899
• ENST00000837362.1:n.128-4441T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-121105170-A-G
• chr12-121105170-A-T

Variant summary

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

The ENST00000837362.1(ENSG00000308932):​n.128-4441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,144 control chromosomes in the GnomAD database, including 51,263 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 0.81 (51263 hom., cov: 32)
• Consequence: ENSG00000308932 ENST00000837362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 9 publications found

Genes affected

ENSG00000308932 (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 (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837362.1. 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
	ENSG00000308932	ENST00000837362.1		n.128-4441T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123639 AN: 152026 Hom.: 51234 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.813 AC: 123716 AN: 152144 Hom.: 51263 Cov.: 32 AF XY: 0.818 AC XY: 60863 AN XY: 74382

African (AFR) AF: 0.640 AC: 26526 AN: 41452

American (AMR) AF: 0.870 AC: 13297 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3202 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4560 AN: 5182

South Asian (SAS) AF: 0.832 AC: 4013 AN: 4826

European-Finnish (FIN) AF: 0.907 AC: 9606 AN: 10586

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59741 AN: 68018

Other (OTH) AF: 0.829 AC: 1753 AN: 2114

Alfa AF: 0.865 Hom.: 30536

Bravo AF: 0.803

Asia WGS AF: 0.846 AC: 2944 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	13
DANN	Benign	0.77
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1794899; hg19: chr12-121542973;