6-84848209-T-C

Variant names:

• chr6-84848209-T-C
• rs7742109

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 0.211 in 152,024 control chromosomes in the GnomAD database, including 3,757 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 0.21 (3757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.888
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32050 AN: 151906 Hom.: 3754 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.211 AC: 32070 AN: 152024 Hom.: 3757 Cov.: 32 AF XY: 0.215 AC XY: 15964 AN XY: 74282

African (AFR) AF: 0.116 AC: 4797 AN: 41516

American (AMR) AF: 0.281 AC: 4293 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1163 AN: 5160

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4804

European-Finnish (FIN) AF: 0.277 AC: 2920 AN: 10546

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16654 AN: 67956

Other (OTH) AF: 0.201 AC: 423 AN: 2106

Alfa AF: 0.199 Hom.: 1254

Bravo AF: 0.207

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.51
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs7742109; hg19: chr6-85557927;