rs4775413

Variant names:

• chr15-61547904-C-T
• rs4775413
• ENST00000559783.2:n.124-40664G>A

Variant summary

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

The ENST00000559783.2(ENSG00000259675):​n.124-40664G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,896 control chromosomes in the GnomAD database, including 14,642 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 0.40 (14642 hom., cov: 31)
• Consequence: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 8 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984782	XR_001751569.2	n.236-40664G>A		intron_variant	Intron 3 of 3
LOC107984782	XR_001751570.2	n.221-40664G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259675	ENST00000559783.2	n.124-40664G>A		intron_variant	Intron 2 of 4	3
ENSG00000259675	ENST00000748013.1	n.347-40664G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61039 AN: 151778 Hom.: 14638 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.402 AC: 61044 AN: 151896 Hom.: 14642 Cov.: 31 AF XY: 0.400 AC XY: 29692 AN XY: 74242

African (AFR) AF: 0.136 AC: 5656 AN: 41444

American (AMR) AF: 0.424 AC: 6478 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1430 AN: 5144

South Asian (SAS) AF: 0.440 AC: 2117 AN: 4808

European-Finnish (FIN) AF: 0.475 AC: 5004 AN: 10532

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 36988 AN: 67930

Other (OTH) AF: 0.432 AC: 906 AN: 2098

Alfa AF: 0.493 Hom.: 46478

Bravo AF: 0.382

Asia WGS AF: 0.351 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.63
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4775413; hg19: chr15-61840103;