6-80873553-C-T

Variant names:

• chr6-80873553-C-T
• rs16892328

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 0.0555 in 151,312 control chromosomes in the GnomAD database, including 286 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 0.055 (286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8397 AN: 151194 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0540

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0455

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0555 AC: 8394 AN: 151312 Hom.: 286 Cov.: 32 AF XY: 0.0561 AC XY: 4150 AN XY: 73912

African (AFR) AF: 0.0151 AC: 620 AN: 41052

American (AMR) AF: 0.110 AC: 1675 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0540 AC: 187 AN: 3462

East Asian (EAS) AF: 0.0782 AC: 401 AN: 5128

South Asian (SAS) AF: 0.0583 AC: 281 AN: 4818

European-Finnish (FIN) AF: 0.0415 AC: 439 AN: 10568

Middle Eastern (MID) AF: 0.0420 AC: 12 AN: 286

European-Non Finnish (NFE) AF: 0.0675 AC: 4580 AN: 67810

Other (OTH) AF: 0.0619 AC: 130 AN: 2100

Alfa AF: 0.0639 Hom.: 422

Bravo AF: 0.0623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs16892328; hg19: chr6-81583270;