6-32551228-C-T

Variant names:

• chr6-32551228-C-T
• rs28490179

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 0.814 in 144,184 control chromosomes in the GnomAD database, including 48,004 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 0.81 (48004 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.828 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: 0.814 AC: 117370 AN: 144174 Hom.: 47999 Cov.: 27

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.894

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.814 AC: 117371 AN: 144184 Hom.: 48004 Cov.: 27 AF XY: 0.812 AC XY: 56813 AN XY: 69950

African (AFR) AF: 0.820 AC: 32109 AN: 39172

American (AMR) AF: 0.841 AC: 11975 AN: 14240

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3102 AN: 3452

East Asian (EAS) AF: 0.774 AC: 3798 AN: 4904

South Asian (SAS) AF: 0.748 AC: 3529 AN: 4716

European-Finnish (FIN) AF: 0.814 AC: 6585 AN: 8086

Middle Eastern (MID) AF: 0.888 AC: 245 AN: 276

European-Non Finnish (NFE) AF: 0.806 AC: 53554 AN: 66442

Other (OTH) AF: 0.845 AC: 1694 AN: 2004

Alfa AF: 0.842 Hom.: 24780

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.15
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs28490179; hg19: chr6-32519005;