rs10484507

Variant names:

• chr6-164185287-A-G
• rs10484507

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 0.0796 in 152,266 control chromosomes in the GnomAD database, including 589 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 0.080 (589 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0796 AC: 12117 AN: 152148 Hom.: 590 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0796 AC: 12117 AN: 152266 Hom.: 589 Cov.: 33 AF XY: 0.0768 AC XY: 5721 AN XY: 74448

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0487

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0754

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0732 Hom.: 244

Bravo AF: 0.0804

Asia WGS AF: 0.0470 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484507; hg19: chr6-164606319;