rs4471448

Variant names:

• chr11-87372282-A-G
• rs4471448
• ENST00000784851.1:n.475+9806A>G

Variant summary

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

The ENST00000784851.1(ENSG00000302190):​n.475+9806A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,090 control chromosomes in the GnomAD database, including 8,195 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 0.30 (8195 hom., cov: 32)
• Consequence: ENSG00000302190 ENST00000784851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 4 publications found

Genes affected

ENSG00000302190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784851.1. 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
	ENSG00000302190	ENST00000784851.1		n.475+9806A>G		intron	N/A
	ENSG00000302190	ENST00000784853.1		n.449-510A>G		intron	N/A
	ENSG00000302212	ENST00000785017.1		n.162-9130T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45746 AN: 151972 Hom.: 8202 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.301 AC: 45726 AN: 152090 Hom.: 8195 Cov.: 32 AF XY: 0.295 AC XY: 21944 AN XY: 74332

African (AFR) AF: 0.125 AC: 5175 AN: 41534

American (AMR) AF: 0.317 AC: 4842 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3470

East Asian (EAS) AF: 0.0890 AC: 460 AN: 5166

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4816

European-Finnish (FIN) AF: 0.330 AC: 3482 AN: 10550

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27853 AN: 67954

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.377 Hom.: 48502

Bravo AF: 0.293

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.60
PhyloP100		0.026

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: rs4471448;

hg19: chr11-87083324;