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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984361	XR_001748316.2	n.318+9806A>G		intron_variant	Intron 2 of 3
LOC107984361	XR_002957260.2	n.319-510A>G		intron_variant	Intron 2 of 7
LOC107984361	XR_002957261.2	n.318+9806A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302190	ENST00000784851.1	n.475+9806A>G		intron_variant	Intron 2 of 2
ENSG00000302190	ENST00000784853.1	n.449-510A>G		intron_variant	Intron 2 of 2
ENSG00000302212	ENST00000785017.1	n.162-9130T>C		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs4471448; hg19: chr11-87083324;