rs282065

chr6-90591645-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.687 in 151,930 control chromosomes in the GnomAD database, including 36,087 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 0.69 (36087 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104272 AN: 151814 Hom.: 36062 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.687 AC: 104345 AN: 151930 Hom.: 36087 Cov.: 31 AF XY: 0.681 AC XY: 50578 AN XY: 74234

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.733

Alfa AF: 0.704 Hom.: 64477

Bravo AF: 0.684

Asia WGS AF: 0.633 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282065; hg19: chr6-91301364; COSMIC: COSV65235352;