rs556025

Variant names:

• chr6-32603103-C-T
• rs556025

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 0.293 in 151,692 control chromosomes in the GnomAD database, including 6,834 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 0.29 (6834 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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: 0.293 AC: 44368 AN: 151574 Hom.: 6835 Cov.: 29

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.293 AC: 44397 AN: 151692 Hom.: 6834 Cov.: 29 AF XY: 0.286 AC XY: 21210 AN XY: 74146

African (AFR) AF: 0.258 AC: 10636 AN: 41300

American (AMR) AF: 0.363 AC: 5530 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5162

South Asian (SAS) AF: 0.248 AC: 1187 AN: 4784

European-Finnish (FIN) AF: 0.199 AC: 2099 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21269 AN: 67892

Other (OTH) AF: 0.317 AC: 668 AN: 2104

Alfa AF: 0.311 Hom.: 617

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.39
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs556025; hg19: chr6-32570880;