chr16-50120902-T-C

Variant names:

• chr16-50120902-T-C
• rs6500291
• ENST00000566770.1:n.125+917A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000566770.1(ENSG00000260381):​n.125+917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,082 control chromosomes in the GnomAD database, including 12,476 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 0.36 (12476 hom., cov: 32)
• Consequence: ENSG00000260381 ENST00000566770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463

Genes affected

ENSG00000260381 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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
ENSG00000260381	ENST00000566770.1	n.125+917A>G		intron_variant	Intron 1 of 2	3
ENSG00000287444	ENST00000657788.1	n.92+747T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54913 AN: 151964 Hom.: 12441 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.362 AC: 54993 AN: 152082 Hom.: 12476 Cov.: 32 AF XY: 0.353 AC XY: 26250 AN XY: 74360

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.337

Alfa AF: 0.276 Hom.: 4141

Bravo AF: 0.391

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6500291; hg19: chr16-50154813;