chr6-51048810-G-A

Variant names:

• chr6-51048810-G-A
• rs10484664

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 0.305 in 152,020 control chromosomes in the GnomAD database, including 7,809 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 0.31 (7809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46434 AN: 151902 Hom.: 7809 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.305 AC: 46442 AN: 152020 Hom.: 7809 Cov.: 32 AF XY: 0.302 AC XY: 22471 AN XY: 74302

African (AFR) AF: 0.176 AC: 7278 AN: 41460

American (AMR) AF: 0.383 AC: 5853 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3466

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5172

South Asian (SAS) AF: 0.352 AC: 1697 AN: 4824

European-Finnish (FIN) AF: 0.316 AC: 3331 AN: 10556

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25254 AN: 67944

Other (OTH) AF: 0.290 AC: 613 AN: 2116

Alfa AF: 0.356 Hom.: 5139

Bravo AF: 0.304

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.29
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10484664; hg19: chr6-51016523;