rs10485227

Variant names:

• chr6-99759451-A-G
• rs10485227

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 0.33 in 151,870 control chromosomes in the GnomAD database, including 9,921 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 0.33 (9921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 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: 0.330 AC: 50139 AN: 151750 Hom.: 9925 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.330 AC: 50144 AN: 151870 Hom.: 9921 Cov.: 32 AF XY: 0.330 AC XY: 24483 AN XY: 74242

African (AFR) AF: 0.112 AC: 4666 AN: 41500

American (AMR) AF: 0.399 AC: 6073 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1647 AN: 3460

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5158

South Asian (SAS) AF: 0.332 AC: 1598 AN: 4818

European-Finnish (FIN) AF: 0.411 AC: 4346 AN: 10568

Middle Eastern (MID) AF: 0.517 AC: 149 AN: 288

European-Non Finnish (NFE) AF: 0.425 AC: 28848 AN: 67836

Other (OTH) AF: 0.374 AC: 787 AN: 2106

Alfa AF: 0.399 Hom.: 52939

Bravo AF: 0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs10485227; hg19: chr6-100207327;