4-126444174-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000286251 (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 (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651327.1. 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
	ENSG00000286251	ENST00000651327.1		n.369-9233C>T		intron	N/A
	ENSG00000286251	ENST00000661809.1		n.515-9233C>T		intron	N/A
	ENSG00000286251	ENST00000826912.1		n.154-9235C>T		intron	N/A

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

African (AFR) AF: 0.196 AC: 8111 AN: 41442

American (AMR) AF: 0.545 AC: 8302 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1963 AN: 3460

East Asian (EAS) AF: 0.411 AC: 2115 AN: 5144

South Asian (SAS) AF: 0.403 AC: 1939 AN: 4806

European-Finnish (FIN) AF: 0.533 AC: 5616 AN: 10546

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44316 AN: 67888

Other (OTH) AF: 0.515 AC: 1083 AN: 2102

Alfa AF: 0.601 Hom.: 123305

Bravo AF: 0.480

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.76
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4833346; hg19: chr4-127365329;