rs1967439

Variant names:

• chr20-50464746-C-T
• rs1967439

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 0.324 in 152,004 control chromosomes in the GnomAD database, including 8,078 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 0.32 (8078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49195 AN: 151886 Hom.: 8072 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.324 AC: 49211 AN: 152004 Hom.: 8078 Cov.: 31 AF XY: 0.323 AC XY: 24003 AN XY: 74300

African (AFR) AF: 0.308 AC: 12764 AN: 41440

American (AMR) AF: 0.388 AC: 5921 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5168

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4810

European-Finnish (FIN) AF: 0.355 AC: 3747 AN: 10568

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22306 AN: 67966

Other (OTH) AF: 0.310 AC: 656 AN: 2116

Alfa AF: 0.325 Hom.: 5847

Bravo AF: 0.328

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.72
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1967439; hg19: chr20-49081283;