rs1408282

Variant names:

• chr6-93142534-G-A
• rs1408282

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 0.1 in 152,090 control chromosomes in the GnomAD database, including 1,005 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 (1005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 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: 0.100 AC: 15229 AN: 151970 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.100 AC: 15230 AN: 152090 Hom.: 1005 Cov.: 32 AF XY: 0.105 AC XY: 7776 AN XY: 74340

African (AFR) AF: 0.0494 AC: 2051 AN: 41510

American (AMR) AF: 0.179 AC: 2730 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3468

East Asian (EAS) AF: 0.191 AC: 983 AN: 5142

South Asian (SAS) AF: 0.243 AC: 1170 AN: 4812

European-Finnish (FIN) AF: 0.0666 AC: 705 AN: 10590

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6802 AN: 67978

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.106 Hom.: 2244

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs1408282; hg19: chr6-93852252;