rs4833346

Variant names:

• chr4-126444174-G-A
• rs4833346
• ENST00000651327.1:n.369-9233C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-126444174-G-A
• chr4-126444174-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651327.1(ENSG00000286251):​n.369-9233C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,834 control chromosomes in the GnomAD database, including 21,099 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 0.49 (21099 hom., cov: 32)
• Consequence: ENSG00000286251 ENST00000651327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

Genes affected

ENSG00000286251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 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
ENSG00000286251	ENST00000651327.1	n.369-9233C>T		intron_variant	Intron 3 of 4
ENSG00000286251	ENST00000661809.1	n.515-9233C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74267 AN: 151716 Hom.: 21093 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.489 AC: 74273 AN: 151834 Hom.: 21099 Cov.: 32 AF XY: 0.483 AC XY: 35843 AN XY: 74164

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.515

Alfa AF: 0.618 Hom.: 60862

Bravo AF: 0.480

Asia WGS AF: 0.417 AC: 1449 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	0.75
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833346; hg19: chr4-127365329;