rs282095

chr6-153941545-C-G

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 0.562 in 152,050 control chromosomes in the GnomAD database, including 24,337 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 0.56 (24337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.563 AC: 85468 AN: 151932 Hom.: 24316 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.562 AC: 85523 AN: 152050 Hom.: 24337 Cov.: 32 AF XY: 0.559 AC XY: 41550 AN XY: 74326

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.561

Alfa AF: 0.582 Hom.: 3193

Bravo AF: 0.553

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.92
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282095; hg19: chr6-154262680; COSMIC: COSV68006997;