rs479536

Positions:

• chr6-32225901-G-A

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 0.0493 in 152,210 control chromosomes in the GnomAD database, including 253 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 0.049 (253 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32225901G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7497 AN: 152092 Hom.: 253 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.00500

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0493 AC: 7497 AN: 152210 Hom.: 253 Cov.: 32 AF XY: 0.0458 AC XY: 3405 AN XY: 74418

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.0759

Gnomad4 ASJ AF: 0.0692

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.00500

Gnomad4 NFE AF: 0.0623

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0547 Hom.: 158

Bravo AF: 0.0560

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs479536; hg19: chr6-32193678;