rs1536215

Variant names:

• chr6-28900138-C-G
• rs1536215

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 0.121 in 151,986 control chromosomes in the GnomAD database, including 1,179 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 0.12 (1179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

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 (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.121 AC: 18435 AN: 151868 Hom.: 1178 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.121 AC: 18459 AN: 151986 Hom.: 1179 Cov.: 32 AF XY: 0.122 AC XY: 9094 AN XY: 74282

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.114

Alfa AF: 0.114 Hom.: 153

Bravo AF: 0.124

Asia WGS AF: 0.140 AC: 484 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	4.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536215; hg19: chr6-28867915;