rs1433396

Variant names:

• chr8-120988362-C-T
• rs1433396
• ENST00000517739.1:n.96-55021C>T

Variant summary

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

The ENST00000517739.1(ENSG00000253619):​n.96-55021C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,102 control chromosomes in the GnomAD database, including 4,243 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 0.21 (4243 hom., cov: 32)
• Consequence: ENSG00000253619 ENST00000517739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 4 publications found

Genes affected

ENSG00000253619 (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 = 0.299 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
ENSG00000253619	ENST00000517739.1	n.96-55021C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32088 AN: 151984 Hom.: 4246 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.211 AC: 32076 AN: 152102 Hom.: 4243 Cov.: 32 AF XY: 0.205 AC XY: 15202 AN XY: 74328

African (AFR) AF: 0.0788 AC: 3273 AN: 41534

American (AMR) AF: 0.216 AC: 3285 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.103 AC: 497 AN: 4832

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10560

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20546 AN: 67968

Other (OTH) AF: 0.248 AC: 523 AN: 2110

Alfa AF: 0.275 Hom.: 7483

Bravo AF: 0.205

Asia WGS AF: 0.0530 AC: 184 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs1433396; hg19: chr8-122000602;