rs10484282

Variant names:

• chr6-129744933-G-A
• rs10484282

Your query was ambiguous. Multiple possible variants found:

• chr6-129744933-G-A
• chr6-129744933-G-C
• chr6-129744933-G-T

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 0.224 in 150,388 control chromosomes in the GnomAD database, including 4,413 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 0.22 (4413 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.224 AC: 33609 AN: 150270 Hom.: 4417 Cov.: 27

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.224 AC: 33614 AN: 150388 Hom.: 4413 Cov.: 27 AF XY: 0.223 AC XY: 16327 AN XY: 73324

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.240

Alfa AF: 0.272 Hom.: 7953

Bravo AF: 0.212

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484282; hg19: chr6-130066078;