rs282108

Variant names:

• chr6-153963783-C-A
• rs282108

Your query was ambiguous. Multiple possible variants found:

• chr6-153963783-C-A
• chr6-153963783-C-G

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 0.8 in 152,150 control chromosomes in the GnomAD database, including 49,075 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 0.80 (49075 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121647 AN: 152034 Hom.: 49049 Cov.: 31

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.800 AC: 121720 AN: 152150 Hom.: 49075 Cov.: 31 AF XY: 0.803 AC XY: 59682 AN XY: 74358

African (AFR) AF: 0.890 AC: 36945 AN: 41534

American (AMR) AF: 0.833 AC: 12716 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2326 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3907 AN: 5166

South Asian (SAS) AF: 0.790 AC: 3813 AN: 4826

European-Finnish (FIN) AF: 0.823 AC: 8704 AN: 10576

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50703 AN: 67992

Other (OTH) AF: 0.780 AC: 1645 AN: 2110

Alfa AF: 0.771 Hom.: 5887

Bravo AF: 0.805

Asia WGS AF: 0.756 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs282108; hg19: chr6-154284918;