chr16-50120902-T-C

Position:

• chr16-50120902-T-C

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, non coding transcript 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: ENST00000566770.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000566770.1	n.125+917A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000657788.1	n.92+747T>C		intron_variant, non_coding_transcript_variant

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;