1-114173741-C-T

Variant names:

• chr1-114173741-C-T
• rs6657718

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 0.21 in 152,014 control chromosomes in the GnomAD database, including 3,662 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 (3662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.210 AC: 31897 AN: 151896 Hom.: 3662 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.210 AC: 31909 AN: 152014 Hom.: 3662 Cov.: 32 AF XY: 0.202 AC XY: 15022 AN XY: 74312

African (AFR) AF: 0.189 AC: 7832 AN: 41446

American (AMR) AF: 0.176 AC: 2685 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3470

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.0806 AC: 388 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17183 AN: 67966

Other (OTH) AF: 0.214 AC: 450 AN: 2102

Alfa AF: 0.209 Hom.: 2243

Bravo AF: 0.211

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.014
DANN	Benign	0.81
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6657718; hg19: chr1-114716363;