rs4537731

Variant names:

• chr11-18047335-T-C
• rs4537731
• ENST00000787024.1:n.97-17713T>C

Variant summary

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

The ENST00000787024.1(ENSG00000302464):​n.97-17713T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,046 control chromosomes in the GnomAD database, including 18,257 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 0.47 (18257 hom., cov: 32)
• Consequence: ENSG00000302464 ENST00000787024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 17 publications found

Genes affected

ENSG00000302464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787024.1. 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
	ENSG00000302464	ENST00000787024.1		n.97-17713T>C		intron	N/A
	ENSG00000302464	ENST00000787025.1		n.98-14603T>C		intron	N/A
	ENSG00000302464	ENST00000787026.1		n.94-14603T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71458 AN: 151928 Hom.: 18210 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.471 AC: 71559 AN: 152046 Hom.: 18257 Cov.: 32 AF XY: 0.462 AC XY: 34321 AN XY: 74316

African (AFR) AF: 0.670 AC: 27758 AN: 41454

American (AMR) AF: 0.368 AC: 5626 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1215 AN: 5188

South Asian (SAS) AF: 0.344 AC: 1657 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4072 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28648 AN: 67962

Other (OTH) AF: 0.455 AC: 961 AN: 2110

Alfa AF: 0.444 Hom.: 5492

Bravo AF: 0.479

Asia WGS AF: 0.325 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.55
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4537731; hg19: chr11-18068882;