rs1892234

Variant names:

• chr14-98254567-G-A
• rs1892234

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 0.563 in 151,980 control chromosomes in the GnomAD database, including 24,453 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 0.56 (24453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

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 (SAS) allele frequency at 95% confidence interval = 0.612 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: 0.563 AC: 85517 AN: 151862 Hom.: 24425 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.563 AC: 85604 AN: 151980 Hom.: 24453 Cov.: 32 AF XY: 0.565 AC XY: 41981 AN XY: 74280

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.538

Alfa AF: 0.558 Hom.: 10739

Bravo AF: 0.561

Asia WGS AF: 0.528 AC: 1839 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	0.23
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1892234; hg19: chr14-98720904;