rs11750584

Variant names:

• chr5-41093757-C-G
• rs11750584
• ENST00000835888.1:n.747-186C>G

Variant summary

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

The ENST00000835888.1(ENSG00000308698):​n.747-186C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,842 control chromosomes in the GnomAD database, including 12,848 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 0.41 (12848 hom., cov: 32)
• Consequence: ENSG00000308698 ENST00000835888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 2 publications found

Genes affected

ENSG00000308698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835888.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308698	ENST00000835888.1		n.747-186C>G		intron	N/A
	ENSG00000308698	ENST00000835889.1		n.654-186C>G		intron	N/A
	ENSG00000308716	ENST00000835937.1		n.199+1965G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61915 AN: 151724 Hom.: 12834 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.408 AC: 61963 AN: 151842 Hom.: 12848 Cov.: 32 AF XY: 0.405 AC XY: 30042 AN XY: 74184

African (AFR) AF: 0.457 AC: 18919 AN: 41370

American (AMR) AF: 0.320 AC: 4885 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.159 AC: 820 AN: 5168

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4810

European-Finnish (FIN) AF: 0.454 AC: 4774 AN: 10522

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28742 AN: 67920

Other (OTH) AF: 0.409 AC: 865 AN: 2114

Alfa AF: 0.421 Hom.: 1682

Bravo AF: 0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs11750584; hg19: chr5-41093859;