chr1-106756611-C-T

Variant names:

• chr1-106756611-C-T
• rs12409858

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 0.161 in 151,966 control chromosomes in the GnomAD database, including 2,170 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 (2170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.161 AC: 24393 AN: 151846 Hom.: 2163 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0759

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.161 AC: 24421 AN: 151966 Hom.: 2170 Cov.: 32 AF XY: 0.161 AC XY: 11984 AN XY: 74272

African (AFR) AF: 0.198 AC: 8222 AN: 41452

American (AMR) AF: 0.151 AC: 2299 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0759 AC: 263 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1462 AN: 5140

South Asian (SAS) AF: 0.192 AC: 927 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10556

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9153 AN: 67958

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.0954 Hom.: 161

Bravo AF: 0.165

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.41
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12409858; hg19: chr1-107299233;