rs4758051

Variant names:

• chr11-8217092-G-A
• rs4758051
• ENST00000825479.1:n.228+368G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-8217092-G-A
• chr11-8217092-G-C

Variant summary

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

The ENST00000825479.1(ENSG00000307368):​n.228+368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,084 control chromosomes in the GnomAD database, including 16,481 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 0.43 (16481 hom., cov: 32)
• Consequence: ENSG00000307368 ENST00000825479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 23 publications found

Genes affected

ENSG00000307368 (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 = 0.546 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
ENSG00000307368	ENST00000825479.1	n.228+368G>A		intron_variant	Intron 3 of 3
ENSG00000307368	ENST00000825480.1	n.240+368G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65293 AN: 151968 Hom.: 16486 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.429 AC: 65285 AN: 152084 Hom.: 16481 Cov.: 32 AF XY: 0.433 AC XY: 32158 AN XY: 74330

African (AFR) AF: 0.145 AC: 6029 AN: 41520

American (AMR) AF: 0.546 AC: 8342 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1851 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2159 AN: 5150

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5556 AN: 10584

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37426 AN: 67944

Other (OTH) AF: 0.450 AC: 951 AN: 2112

Alfa AF: 0.513 Hom.: 87685

Bravo AF: 0.418

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.59
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs4758051; hg19: chr11-8238639;