14-38626363-A-G

Variant names:

• chr14-38626363-A-G
• rs1449720

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.468 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

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.452

Alfa AF: 0.445 Hom.: 8972

Bravo AF: 0.484

Asia WGS AF: 0.623 AC: 2153 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449720; hg19: chr14-39095567;