rs4758405

Variant names:

• chr11-6303404-G-A
• rs4758405
• ENST00000833324.1:n.138-8090C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-6303404-G-A
• chr11-6303404-G-C
• chr11-6303404-G-T

Variant summary

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

The ENST00000833324.1(ENSG00000308330):​n.138-8090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,008 control chromosomes in the GnomAD database, including 18,978 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 (18978 hom., cov: 33)
• Consequence: ENSG00000308330 ENST00000833324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 5 publications found

Genes affected

ENSG00000308330 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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
ENSG00000308330	ENST00000833324.1	n.138-8090C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74884 AN: 151890 Hom.: 18940 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.493 AC: 74978 AN: 152008 Hom.: 18978 Cov.: 33 AF XY: 0.494 AC XY: 36721 AN XY: 74310

African (AFR) AF: 0.612 AC: 25344 AN: 41442

American (AMR) AF: 0.479 AC: 7326 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2052 AN: 3472

East Asian (EAS) AF: 0.429 AC: 2221 AN: 5176

South Asian (SAS) AF: 0.359 AC: 1730 AN: 4816

European-Finnish (FIN) AF: 0.542 AC: 5714 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29063 AN: 67962

Other (OTH) AF: 0.501 AC: 1058 AN: 2110

Alfa AF: 0.456 Hom.: 28509

Bravo AF: 0.499

Asia WGS AF: 0.443 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.49
DANN	Benign	0.70
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4758405; hg19: chr11-6324634;