rs888419

Variant names:

• chr14-74622392-A-G
• rs888419

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 0.411 in 152,154 control chromosomes in the GnomAD database, including 13,900 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 0.41 (13900 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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: 0.411 AC: 62483 AN: 152034 Hom.: 13892 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.411 AC: 62517 AN: 152154 Hom.: 13900 Cov.: 33 AF XY: 0.411 AC XY: 30551 AN XY: 74382

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.420

Alfa AF: 0.480 Hom.: 17827

Bravo AF: 0.407

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888419; hg19: chr14-75089095;