rs4530856

chr6-46217747-A-C

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 152,162 control chromosomes in the GnomAD database, including 1,495 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 (1495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18439 AN: 152044 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.121 AC: 18455 AN: 152162 Hom.: 1495 Cov.: 32 AF XY: 0.123 AC XY: 9164 AN XY: 74400

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.131

Alfa AF: 0.121 Hom.: 703

Bravo AF: 0.132

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	5.6
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4530856; hg19: chr6-46185484;