rs12133603

Variant names:

• chr1-234927823-C-A
• rs12133603
• ENST00000850484.1:n.995C>A

Variant summary

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

The ENST00000850484.1(ENSG00000310502):​n.995C>A 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 0.13 in 152,114 control chromosomes in the GnomAD database, including 1,489 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 0.13 (1489 hom., cov: 31)
• Consequence: ENSG00000310502 ENST00000850484.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 1 publications found

Genes affected

ENSG00000310502 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850484.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310502	ENST00000850484.1		n.995C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000310502	ENST00000850485.1		n.772C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000310502	ENST00000850486.1		n.932C>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19803 AN: 151996 Hom.: 1490 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.130 AC: 19807 AN: 152114 Hom.: 1489 Cov.: 31 AF XY: 0.132 AC XY: 9826 AN XY: 74390

African (AFR) AF: 0.101 AC: 4208 AN: 41480

American (AMR) AF: 0.0847 AC: 1296 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0712 AC: 343 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2647 AN: 10568

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10654 AN: 67966

Other (OTH) AF: 0.112 AC: 236 AN: 2116

Alfa AF: 0.140 Hom.: 549

Bravo AF: 0.114

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.71
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12133603;

hg19: chr1-235063570;