rs4983559

Positions:

• chr14-104810872-G-A
• chr14-104810872-G-C

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 0.524 in 151,282 control chromosomes in the GnomAD database, including 21,697 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 0.52 (21697 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79237 AN: 151164 Hom.: 21671 Cov.: 29

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.524 AC: 79306 AN: 151282 Hom.: 21697 Cov.: 29 AF XY: 0.519 AC XY: 38316 AN XY: 73838

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.539

Alfa AF: 0.590 Hom.: 49952

Bravo AF: 0.514

Asia WGS AF: 0.313 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4983559; hg19: chr14-105277209;