rs10498478

Variant names:

• chr14-55779323-A-G
• rs10498478

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 0.0207 in 152,202 control chromosomes in the GnomAD database, including 76 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 0.021 (76 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.065 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: 0.0206 AC: 3137 AN: 152084 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.00543

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0207 AC: 3147 AN: 152202 Hom.: 76 Cov.: 32 AF XY: 0.0232 AC XY: 1726 AN XY: 74412

Gnomad4 AFR AF: 0.00542

Gnomad4 AMR AF: 0.0684

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.0353

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0184 Hom.: 0

Bravo AF: 0.0238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498478; hg19: chr14-56246041;