14-38626363-A-G

Variant names:

• chr14-38626363-A-G
• rs1449720

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 0.469 in 151,888 control chromosomes in the GnomAD database, including 17,154 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 0.47 (17154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.468 AC: 71091 AN: 151770 Hom.: 17120 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.469 AC: 71187 AN: 151888 Hom.: 17154 Cov.: 32 AF XY: 0.474 AC XY: 35196 AN XY: 74240

African (AFR) AF: 0.477 AC: 19758 AN: 41416

American (AMR) AF: 0.555 AC: 8479 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1218 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4010 AN: 5170

South Asian (SAS) AF: 0.528 AC: 2549 AN: 4824

European-Finnish (FIN) AF: 0.446 AC: 4688 AN: 10512

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 29011 AN: 67916

Other (OTH) AF: 0.452 AC: 955 AN: 2114

Alfa AF: 0.455 Hom.: 14188

Bravo AF: 0.484

Asia WGS AF: 0.623 AC: 2153 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.78
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1449720; hg19: chr14-39095567;