1-50409158-T-C

Variant names:

• chr1-50409158-T-C
• rs2784143

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.695 AC: 28861 AN: 41500

American (AMR) AF: 0.858 AC: 13110 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2761 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4284 AN: 5176

South Asian (SAS) AF: 0.873 AC: 4215 AN: 4826

European-Finnish (FIN) AF: 0.873 AC: 9254 AN: 10598

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56109 AN: 67930

Other (OTH) AF: 0.811 AC: 1713 AN: 2112

Alfa AF: 0.816 Hom.: 128406

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2784143; hg19: chr1-50874830;