16-50818521-T-C

Position:

• chr16-50818521-T-C

Variant summary

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

The variant allele was found at a frequency of 0.961 in 152,168 control chromosomes in the GnomAD database, including 70,486 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 0.96 (70486 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50818521T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146127 AN: 152048 Hom.: 70428 Cov.: 30

Gnomad AFR AF: 0.984

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.961 AC: 146248 AN: 152168 Hom.: 70486 Cov.: 30 AF XY: 0.956 AC XY: 71127 AN XY: 74390

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.953

Alfa AF: 0.971 Hom.: 6005

Bravo AF: 0.968

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.068
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032687; hg19: chr16-50852432;