1-162064100-C-T

Variant names:

• chr1-162064100-C-T
• rs12143842

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 0.224 in 151,998 control chromosomes in the GnomAD database, including 4,398 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 0.22 (4398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 94 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 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: 0.224 AC: 34094 AN: 151880 Hom.: 4400 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.224 AC: 34089 AN: 151998 Hom.: 4398 Cov.: 32 AF XY: 0.227 AC XY: 16895 AN XY: 74302

African (AFR) AF: 0.124 AC: 5133 AN: 41456

American (AMR) AF: 0.222 AC: 3397 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3466

East Asian (EAS) AF: 0.353 AC: 1828 AN: 5172

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4814

European-Finnish (FIN) AF: 0.248 AC: 2612 AN: 10538

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17243 AN: 67952

Other (OTH) AF: 0.234 AC: 493 AN: 2106

Alfa AF: 0.249 Hom.: 22379

Bravo AF: 0.215

Asia WGS AF: 0.351 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs12143842; hg19: chr1-162033890;