6-32551228-C-T

Variant names:

• chr6-32551228-C-T
• rs28490179

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 0.814 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.845

Alfa AF: 0.844 Hom.: 13100

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28490179; hg19: chr6-32519005;