14-23629422-C-T

Variant names:

• chr14-23629422-C-T
• rs222723

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 0.74 in 152,154 control chromosomes in the GnomAD database, including 42,496 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 0.74 (42496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.740 AC: 112554 AN: 152036 Hom.: 42484 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.740 AC: 112604 AN: 152154 Hom.: 42496 Cov.: 32 AF XY: 0.741 AC XY: 55117 AN XY: 74394

African (AFR) AF: 0.574 AC: 23816 AN: 41482

American (AMR) AF: 0.782 AC: 11957 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2720 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4212 AN: 5172

South Asian (SAS) AF: 0.714 AC: 3446 AN: 4826

European-Finnish (FIN) AF: 0.818 AC: 8663 AN: 10594

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55209 AN: 68008

Other (OTH) AF: 0.756 AC: 1598 AN: 2114

Alfa AF: 0.786 Hom.: 40157

Bravo AF: 0.730

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs222723; hg19: chr14-24098631;