6-105635831-A-G

Variant names:

• chr6-105635831-A-G
• rs10484468

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 0.102 in 152,244 control chromosomes in the GnomAD database, including 1,462 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 0.10 (1462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15461 AN: 152126 Hom.: 1452 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.102 AC: 15501 AN: 152244 Hom.: 1462 Cov.: 32 AF XY: 0.106 AC XY: 7856 AN XY: 74446

African (AFR) AF: 0.224 AC: 9302 AN: 41546

American (AMR) AF: 0.0898 AC: 1373 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 71 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5164

South Asian (SAS) AF: 0.101 AC: 488 AN: 4822

European-Finnish (FIN) AF: 0.0900 AC: 956 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0220 AC: 1495 AN: 68008

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0756 Hom.: 133

Bravo AF: 0.109

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.50
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10484468; hg19: chr6-106083706;