rs4983382

chr14-104723167-G-A

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 0.818 in 152,198 control chromosomes in the GnomAD database, including 51,297 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 0.82 (51297 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124398 AN: 152080 Hom.: 51251 Cov.: 34

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.818 AC: 124499 AN: 152198 Hom.: 51297 Cov.: 34 AF XY: 0.818 AC XY: 60892 AN XY: 74424

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.829

Alfa AF: 0.774 Hom.: 64353

Bravo AF: 0.831

Asia WGS AF: 0.850 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4983382; hg19: chr14-105189504;