rs10483376

Variant names:

• chr14-30328579-A-G
• rs10483376

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 0.0365 in 152,268 control chromosomes in the GnomAD database, including 294 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 0.036 (294 hom., cov: 32)
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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: 0.0363 AC: 5528 AN: 152150 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0178

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00270

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0365 AC: 5556 AN: 152268 Hom.: 294 Cov.: 32 AF XY: 0.0359 AC XY: 2676 AN XY: 74468

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.00271

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0218 Hom.: 19

Bravo AF: 0.0399

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483376; hg19: chr14-30797785;