rs28421666

Variant names:

• chr6-32624960-A-G
• rs28421666

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 0.0675 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
• Publications: 47 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.111 AC: 4429 AN: 40050

American (AMR) AF: 0.0862 AC: 1277 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.00930 AC: 31 AN: 3334

East Asian (EAS) AF: 0.107 AC: 547 AN: 5092

South Asian (SAS) AF: 0.0503 AC: 232 AN: 4612

European-Finnish (FIN) AF: 0.120 AC: 1179 AN: 9848

Middle Eastern (MID) AF: 0.0352 AC: 10 AN: 284

European-Non Finnish (NFE) AF: 0.0315 AC: 2083 AN: 66048

Other (OTH) AF: 0.0594 AC: 118 AN: 1986

Alfa AF: 0.0423 Hom.: 748

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs28421666; hg19: chr6-32592737;