rs282135

Variant names:

• chr6-89242511-G-T
• rs282135

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 0.783 in 152,144 control chromosomes in the GnomAD database, including 47,247 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 0.78 (47247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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: 0.783 AC: 119105 AN: 152026 Hom.: 47215 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.783 AC: 119190 AN: 152144 Hom.: 47247 Cov.: 32 AF XY: 0.785 AC XY: 58355 AN XY: 74382

African (AFR) AF: 0.918 AC: 38131 AN: 41548

American (AMR) AF: 0.692 AC: 10570 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2322 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3733 AN: 5176

South Asian (SAS) AF: 0.693 AC: 3334 AN: 4812

European-Finnish (FIN) AF: 0.790 AC: 8357 AN: 10572

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50229 AN: 67964

Other (OTH) AF: 0.759 AC: 1605 AN: 2116

Alfa AF: 0.748 Hom.: 21691

Bravo AF: 0.780

Asia WGS AF: 0.754 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.059
DANN	Benign	0.37
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs282135; hg19: chr6-89952230;