rs282095

Variant names:

• chr6-153941545-C-G
• rs282095

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 0.562 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.489 AC: 20276 AN: 41462

American (AMR) AF: 0.490 AC: 7484 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2271 AN: 5166

South Asian (SAS) AF: 0.497 AC: 2393 AN: 4818

European-Finnish (FIN) AF: 0.641 AC: 6756 AN: 10546

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42590 AN: 67988

Other (OTH) AF: 0.561 AC: 1186 AN: 2114

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
PhyloP100		-0.74

Splicing

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

Other links and lift over

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