rs4981283

Variant names:

• chr14-35340878-A-G
• rs4981283

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 0.505 in 152,024 control chromosomes in the GnomAD database, including 19,684 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 0.51 (19684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.505 AC: 76767 AN: 151906 Hom.: 19671 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.505 AC: 76825 AN: 152024 Hom.: 19684 Cov.: 32 AF XY: 0.509 AC XY: 37851 AN XY: 74298

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.499

Alfa AF: 0.507 Hom.: 7253

Bravo AF: 0.496

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4981283; hg19: chr14-35810084;