1-50409158-T-C

Position:

• chr1-50409158-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 0.798 in 152,096 control chromosomes in the GnomAD database, including 48,789 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 0.80 (48789 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50409158T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121275 AN: 151978 Hom.: 48767 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.798 AC: 121343 AN: 152096 Hom.: 48789 Cov.: 32 AF XY: 0.802 AC XY: 59675 AN XY: 74364

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.811

Alfa AF: 0.820 Hom.: 48775

Bravo AF: 0.791

Asia WGS AF: 0.803 AC: 2784 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2784143; hg19: chr1-50874830;