16-50805737-T-C

Position:

• chr16-50805737-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 0.552 in 152,022 control chromosomes in the GnomAD database, including 24,015 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 0.55 (24015 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50805737T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83892 AN: 151904 Hom.: 23977 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.552 AC: 83986 AN: 152022 Hom.: 24015 Cov.: 31 AF XY: 0.548 AC XY: 40734 AN XY: 74294

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.541

Alfa AF: 0.544 Hom.: 5000

Bravo AF: 0.558

Asia WGS AF: 0.384 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861762; hg19: chr16-50839648;