rs10484282

Positions:

• chr6-129744933-G-A
• chr6-129744933-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 0.224 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;