rs1536215

Variant names:

• chr6-28900138-C-G
• rs1536215

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 0.121 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
• Publications: 8 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 (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

African (AFR) AF: 0.126 AC: 5227 AN: 41454

American (AMR) AF: 0.122 AC: 1871 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3466

East Asian (EAS) AF: 0.187 AC: 962 AN: 5150

South Asian (SAS) AF: 0.138 AC: 662 AN: 4810

European-Finnish (FIN) AF: 0.128 AC: 1343 AN: 10528

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7723 AN: 67972

Other (OTH) AF: 0.114 AC: 241 AN: 2114

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1536215; hg19: chr6-28867915;