rs1950809

Variant names:

• chr14-92218276-T-C
• rs1950809

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 0.712 in 151,870 control chromosomes in the GnomAD database, including 38,978 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 0.71 (38978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108034 AN: 151752 Hom.: 38962 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.712 AC: 108100 AN: 151870 Hom.: 38978 Cov.: 32 AF XY: 0.715 AC XY: 53051 AN XY: 74196

African (AFR) AF: 0.583 AC: 24140 AN: 41430

American (AMR) AF: 0.797 AC: 12165 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4355 AN: 5182

South Asian (SAS) AF: 0.710 AC: 3419 AN: 4814

European-Finnish (FIN) AF: 0.762 AC: 7976 AN: 10468

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51066 AN: 67918

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.739 Hom.: 16006

Bravo AF: 0.711

Asia WGS AF: 0.795 AC: 2752 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1950809; hg19: chr14-92684620;