6-80873553-C-T

Variant names:

• chr6-80873553-C-T
• rs16892328

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 0.0555 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0555 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

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0540

Gnomad4 EAS AF: 0.0782

Gnomad4 SAS AF: 0.0583

Gnomad4 FIN AF: 0.0415

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.0619

Alfa AF: 0.0637 Hom.: 361

Bravo AF: 0.0623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16892328; hg19: chr6-81583270;