rs10484664

Variant names:

• chr6-51048810-G-A
• rs10484664

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 0.305 in 152,020 control chromosomes in the GnomAD database, including 7,809 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 0.31 (7809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 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: 0.306 AC: 46434 AN: 151902 Hom.: 7809 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.305 AC: 46442 AN: 152020 Hom.: 7809 Cov.: 32 AF XY: 0.302 AC XY: 22471 AN XY: 74302

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.290

Alfa AF: 0.356 Hom.: 4662

Bravo AF: 0.304

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484664; hg19: chr6-51016523;