1-97009739-C-T

Variant names:

• chr1-97009739-C-T
• rs12123160

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0228 in 152,276 control chromosomes in the GnomAD database, including 47 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 0.023 (47 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0228 (3478/152276) while in subpopulation NFE AF = 0.0325 (2214/68022). AF 95% confidence interval is 0.0314. There are 47 homozygotes in GnomAd4. There are 1631 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0229 AC: 3481 AN: 152158 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00982

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0325

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0228 AC: 3478 AN: 152276 Hom.: 47 Cov.: 33 AF XY: 0.0219 AC XY: 1631 AN XY: 74456

African (AFR) AF: 0.00977 AC: 406 AN: 41562

American (AMR) AF: 0.0216 AC: 330 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0267 AC: 129 AN: 4826

European-Finnish (FIN) AF: 0.0229 AC: 243 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0325 AC: 2214 AN: 68022

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0183 Hom.: 11

Bravo AF: 0.0222

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs12123160; hg19: chr1-97475295;