chr6-84672210-C-T

Variant names:

• chr6-84672210-C-T
• rs6454393

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 0.16 in 152,102 control chromosomes in the GnomAD database, including 2,594 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 0.16 (2594 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 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: 0.160 AC: 24335 AN: 151984 Hom.: 2573 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00502

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.160 AC: 24388 AN: 152102 Hom.: 2594 Cov.: 31 AF XY: 0.158 AC XY: 11718 AN XY: 74360

African (AFR) AF: 0.295 AC: 12251 AN: 41468

American (AMR) AF: 0.107 AC: 1634 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3466

East Asian (EAS) AF: 0.00503 AC: 26 AN: 5170

South Asian (SAS) AF: 0.104 AC: 503 AN: 4816

European-Finnish (FIN) AF: 0.107 AC: 1131 AN: 10582

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7907 AN: 67996

Other (OTH) AF: 0.149 AC: 314 AN: 2106

Alfa AF: 0.123 Hom.: 2226

Bravo AF: 0.165

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	19
DANN	Benign	0.55
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6454393; hg19: chr6-85381928;