rs10484564

Variant names:

• chr6-32784272-G-C
• rs10484564

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 0.05 in 152,238 control chromosomes in the GnomAD database, including 287 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 0.050 (287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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 (NFE) allele frequency at 95% confidence interval = 0.0743 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: 0.0501 AC: 7621 AN: 152120 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0500 AC: 7613 AN: 152238 Hom.: 287 Cov.: 32 AF XY: 0.0484 AC XY: 3602 AN XY: 74446

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0445

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0461

Gnomad4 NFE AF: 0.0760

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0624 Hom.: 52

Bravo AF: 0.0483

Asia WGS AF: 0.0220 AC: 76 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484564; hg19: chr6-32752049;