1-172646255-C-T

Variant names:

• chr1-172646255-C-T
• rs1492899

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 0.503 in 151,974 control chromosomes in the GnomAD database, including 20,142 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 0.50 (20142 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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: 0.503 AC: 76364 AN: 151856 Hom.: 20097 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.503 AC: 76466 AN: 151974 Hom.: 20142 Cov.: 31 AF XY: 0.504 AC XY: 37415 AN XY: 74268

African (AFR) AF: 0.674 AC: 27910 AN: 41430

American (AMR) AF: 0.425 AC: 6501 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1908 AN: 5160

South Asian (SAS) AF: 0.540 AC: 2593 AN: 4802

European-Finnish (FIN) AF: 0.500 AC: 5276 AN: 10550

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29458 AN: 67966

Other (OTH) AF: 0.478 AC: 1008 AN: 2110

Alfa AF: 0.449 Hom.: 45764

Bravo AF: 0.499

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.46
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1492899; hg19: chr1-172615395;