16-52550383-T-G

Variant names:

• chr16-52550383-T-G
• rs3095607
• ENST00000826650.1:n.102+3871T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000826650.1(ENSG00000285800):​n.102+3871T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,136 control chromosomes in the GnomAD database, including 11,293 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 0.37 (11293 hom., cov: 33)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 3 publications found

Genes affected

ENSG00000285800 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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+3871T>G		intron_variant	Intron 1 of 2
ENSG00000285800	ENST00000826651.1	n.89+3871T>G		intron_variant	Intron 1 of 5
ENSG00000285800	ENST00000826652.1	n.104+3823T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55800 AN: 152018 Hom.: 11260 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.367 AC: 55898 AN: 152136 Hom.: 11293 Cov.: 33 AF XY: 0.370 AC XY: 27526 AN XY: 74372

African (AFR) AF: 0.518 AC: 21477 AN: 41478

American (AMR) AF: 0.384 AC: 5873 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3215 AN: 5182

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4830

European-Finnish (FIN) AF: 0.317 AC: 3347 AN: 10572

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18194 AN: 68004

Other (OTH) AF: 0.363 AC: 766 AN: 2112

Alfa AF: 0.311 Hom.: 4074

Bravo AF: 0.383

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	19
DANN	Benign	0.76
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs3095607; hg19: chr16-52584295;