rs605928

Variant names:

• chr15-58753964-C-G
• rs605928
• ENST00000671030.1:n.213+3829C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-58753964-C-G
• chr15-58753964-C-T

Variant summary

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

The ENST00000671030.1(ENSG00000286897):​n.213+3829C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,124 control chromosomes in the GnomAD database, including 18,902 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 0.46 (18902 hom., cov: 33)
• Consequence: ENSG00000286897 ENST00000671030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 4 publications found

Genes affected

ENSG00000286897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 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
ENSG00000286897	ENST00000671030.1	n.213+3829C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70317 AN: 152006 Hom.: 18851 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.463 AC: 70432 AN: 152124 Hom.: 18902 Cov.: 33 AF XY: 0.472 AC XY: 35093 AN XY: 74344

African (AFR) AF: 0.698 AC: 28935 AN: 41482

American (AMR) AF: 0.461 AC: 7054 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4472 AN: 5190

South Asian (SAS) AF: 0.512 AC: 2469 AN: 4826

European-Finnish (FIN) AF: 0.448 AC: 4731 AN: 10550

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20460 AN: 68000

Other (OTH) AF: 0.421 AC: 890 AN: 2112

Alfa AF: 0.199 Hom.: 395

Bravo AF: 0.478

Asia WGS AF: 0.684 AC: 2375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.38
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs605928; hg19: chr15-59046163;