rs10484564

chr6-32784272-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 0.05 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;