rs10483640

Positions:

• chr14-55223031-G-A
• chr14-55223031-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 0.0926 in 152,202 control chromosomes in the GnomAD database, including 1,780 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 0.093 (1780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

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 = 0.278 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: 0.0924 AC: 14053 AN: 152084 Hom.: 1769 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.00803

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0926 AC: 14101 AN: 152202 Hom.: 1780 Cov.: 32 AF XY: 0.0899 AC XY: 6692 AN XY: 74418

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.0636

Gnomad4 FIN AF: 0.00509

Gnomad4 NFE AF: 0.00803

Gnomad4 OTH AF: 0.0775

Alfa AF: 0.00584 Hom.: 11

Bravo AF: 0.103

Asia WGS AF: 0.0860 AC: 298 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	0.37
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483640; hg19: chr14-55689749;