rs10498345

chr14-38551301-T-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 0.0643 in 152,232 control chromosomes in the GnomAD database, including 692 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 0.064 (692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 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: 0.0644 AC: 9792 AN: 152114 Hom.: 691 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00300

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0643 AC: 9796 AN: 152232 Hom.: 692 Cov.: 32 AF XY: 0.0686 AC XY: 5104 AN XY: 74428

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.0255

Gnomad4 NFE AF: 0.00300

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0195 Hom.: 136

Bravo AF: 0.0764

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	3.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498345; hg19: chr14-39020505;