rs4354815

Variant names:

• chr13-80993818-A-G
• rs4354815
• ENST00000655229.1:n.43-7339T>C

Variant summary

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

The ENST00000655229.1(ENSG00000286746):​n.43-7339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,256 control chromosomes in the GnomAD database, including 458 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 0.055 (458 hom., cov: 32)
• Consequence: ENSG00000286746 ENST00000655229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 0 publications found

Genes affected

ENSG00000286746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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
ENSG00000286746	ENST00000655229.1	n.43-7339T>C		intron_variant	Intron 1 of 1
ENSG00000286746	ENST00000660876.1	n.53+23862T>C		intron_variant	Intron 1 of 1
ENSG00000286746	ENST00000661648.1	n.30+23862T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8317 AN: 152138 Hom.: 461 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0487

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

GnomAD4 genome AF: 0.0547 AC: 8321 AN: 152256 Hom.: 458 Cov.: 32 AF XY: 0.0525 AC XY: 3910 AN XY: 74446

African (AFR) AF: 0.140 AC: 5811 AN: 41528

American (AMR) AF: 0.0317 AC: 484 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4828

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10618

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0217 AC: 1476 AN: 68020

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0387 Hom.: 63

Bravo AF: 0.0621

Asia WGS AF: 0.0190 AC: 64 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.75
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4354815; hg19: chr13-81567953;