rs6433104

Variant names:

• chr2-150994352-T-C
• rs6433104
• ENST00000425983.1:n.172-812T>C

Variant summary

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

The ENST00000425983.1(ENSG00000228064):​n.172-812T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,158 control chromosomes in the GnomAD database, including 55,259 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 0.84 (55259 hom., cov: 32)
• Consequence: ENSG00000228064 ENST00000425983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 2 publications found

Genes affected

ENSG00000228064 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228064	ENST00000425983.1	n.172-812T>C		intron_variant	Intron 2 of 3	5
ENSG00000222031	ENST00000812493.1	n.182-17057A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128029 AN: 152040 Hom.: 55221 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.842 AC: 128117 AN: 152158 Hom.: 55259 Cov.: 32 AF XY: 0.845 AC XY: 62881 AN XY: 74404

African (AFR) AF: 0.639 AC: 26466 AN: 41438

American (AMR) AF: 0.903 AC: 13816 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3074 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4900 AN: 5186

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4826

European-Finnish (FIN) AF: 0.961 AC: 10196 AN: 10610

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.922 AC: 62722 AN: 68010

Other (OTH) AF: 0.860 AC: 1819 AN: 2114

Alfa AF: 0.888 Hom.: 16253

Bravo AF: 0.831

Asia WGS AF: 0.872 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.50
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs6433104; hg19: chr2-151850866;