6-170110297-A-G

Variant names:

• chr6-170110297-A-G
• rs10946292

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 0.265 in 152,162 control chromosomes in the GnomAD database, including 6,525 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 0.26 (6525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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: 0.265 AC: 40224 AN: 152044 Hom.: 6495 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.265 AC: 40322 AN: 152162 Hom.: 6525 Cov.: 33 AF XY: 0.267 AC XY: 19838 AN XY: 74416

African (AFR) AF: 0.454 AC: 18836 AN: 41486

American (AMR) AF: 0.246 AC: 3761 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1798 AN: 5154

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10610

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11098 AN: 68002

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.186 Hom.: 5101

Bravo AF: 0.276

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10946292; hg19: chr6-170425521;