rs3112578

Variant names:

• chr16-52551528-C-T
• rs3112578
• ENST00000826650.1:n.102+5016C>T

Variant summary

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

The ENST00000826650.1(ENSG00000285800):​n.102+5016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,004 control chromosomes in the GnomAD database, including 36,691 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 0.69 (36691 hom., cov: 32)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 3 publications found

Genes affected

ENSG00000285800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 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
ENSG00000285800	ENST00000826650.1	n.102+5016C>T		intron_variant	Intron 1 of 2
ENSG00000285800	ENST00000826651.1	n.89+5016C>T		intron_variant	Intron 1 of 5
ENSG00000285800	ENST00000826652.1	n.104+4968C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105006 AN: 151886 Hom.: 36683 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.691 AC: 105055 AN: 152004 Hom.: 36691 Cov.: 32 AF XY: 0.690 AC XY: 51292 AN XY: 74298

African (AFR) AF: 0.604 AC: 25046 AN: 41440

American (AMR) AF: 0.651 AC: 9941 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2370 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2738 AN: 5154

South Asian (SAS) AF: 0.786 AC: 3784 AN: 4812

European-Finnish (FIN) AF: 0.739 AC: 7803 AN: 10556

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51076 AN: 67972

Other (OTH) AF: 0.686 AC: 1449 AN: 2112

Alfa AF: 0.725 Hom.: 26319

Bravo AF: 0.677

Asia WGS AF: 0.662 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.45
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3112578; hg19: chr16-52585440;