rs28421666

chr6-32624960-A-G

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 0.0675 in 146,902 control chromosomes in the GnomAD database, including 469 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 0.068 (469 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 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: 0.0675 AC: 9907 AN: 146796 Hom.: 468 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0119

Gnomad AMR AF: 0.0856

Gnomad ASJ AF: 0.00930

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0327

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0675 AC: 9916 AN: 146902 Hom.: 469 Cov.: 31 AF XY: 0.0717 AC XY: 5143 AN XY: 71746

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.00930

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0503

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.0594

Alfa AF: 0.0374 Hom.: 218

Bravo AF: 0.0672

Asia WGS AF: 0.0860 AC: 294 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	11
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28421666; hg19: chr6-32592737;