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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0959 AC: 3935 AN: 41028

American (AMR) AF: 0.205 AC: 3078 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1258 AN: 3458

East Asian (EAS) AF: 0.133 AC: 667 AN: 4998

South Asian (SAS) AF: 0.173 AC: 813 AN: 4712

European-Finnish (FIN) AF: 0.315 AC: 3236 AN: 10274

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19768 AN: 67580

Other (OTH) AF: 0.240 AC: 500 AN: 2084

Alfa AF: 0.264 Hom.: 17048

Bravo AF: 0.212

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs10484282; hg19: chr6-130066078;