rs4465523

Variant names:

• chr14-20445364-G-A
• rs4465523
• ENST00000800201.1:n.367-1880G>A

Variant summary

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

The ENST00000800201.1(ENSG00000291038):​n.367-1880G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,998 control chromosomes in the GnomAD database, including 9,222 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 0.34 (9222 hom., cov: 32)
• Consequence: ENSG00000291038 ENST00000800201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 16 publications found

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291038	ENST00000800201.1	n.367-1880G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52208 AN: 151880 Hom.: 9221 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.344 AC: 52225 AN: 151998 Hom.: 9222 Cov.: 32 AF XY: 0.348 AC XY: 25837 AN XY: 74276

African (AFR) AF: 0.308 AC: 12765 AN: 41424

American (AMR) AF: 0.264 AC: 4027 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1902 AN: 5162

South Asian (SAS) AF: 0.470 AC: 2261 AN: 4810

European-Finnish (FIN) AF: 0.429 AC: 4528 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23856 AN: 67988

Other (OTH) AF: 0.369 AC: 781 AN: 2114

Alfa AF: 0.352 Hom.: 40455

Bravo AF: 0.325

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.6
DANN	Benign	0.77
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs4465523; hg19: chr14-20913523;