rs11933661

Variant names:

• chr4-130091985-C-T
• rs11933661
• ENST00000839037.1:n.435-32147C>T

Variant summary

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

The ENST00000839037.1(ENSG00000309145):​n.435-32147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,072 control chromosomes in the GnomAD database, including 24,489 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 0.55 (24489 hom., cov: 32)
• Consequence: ENSG00000309145 ENST00000839037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 9 publications found

Genes affected

ENSG00000309145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839037.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309145	ENST00000839037.1		n.435-32147C>T		intron	N/A
	ENSG00000309145	ENST00000839038.1		n.431+547C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83767 AN: 151954 Hom.: 24450 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.552 AC: 83872 AN: 152072 Hom.: 24489 Cov.: 32 AF XY: 0.550 AC XY: 40882 AN XY: 74330

African (AFR) AF: 0.753 AC: 31239 AN: 41512

American (AMR) AF: 0.543 AC: 8295 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3284 AN: 5146

South Asian (SAS) AF: 0.416 AC: 2006 AN: 4818

European-Finnish (FIN) AF: 0.445 AC: 4694 AN: 10558

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31020 AN: 67962

Other (OTH) AF: 0.553 AC: 1168 AN: 2114

Alfa AF: 0.496 Hom.: 77946

Bravo AF: 0.573

Asia WGS AF: 0.522 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.25
PhyloP100		-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11933661;

hg19: chr4-131013140;