chr1-54752234-T-C

Variant names:

• chr1-54752234-T-C
• rs2873551

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 0.364 in 152,080 control chromosomes in the GnomAD database, including 10,351 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 0.36 (10351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.548 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: 0.364 AC: 55281 AN: 151962 Hom.: 10339 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.364 AC: 55318 AN: 152080 Hom.: 10351 Cov.: 33 AF XY: 0.362 AC XY: 26913 AN XY: 74304

African (AFR) AF: 0.305 AC: 12650 AN: 41482

American (AMR) AF: 0.434 AC: 6629 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2918 AN: 5168

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4824

European-Finnish (FIN) AF: 0.348 AC: 3673 AN: 10568

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25369 AN: 67982

Other (OTH) AF: 0.355 AC: 750 AN: 2114

Alfa AF: 0.370 Hom.: 28312

Bravo AF: 0.378

Asia WGS AF: 0.404 AC: 1404 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	2.9
DANN	Benign	0.56
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2873551; hg19: chr1-55217907; COSMIC: COSV107469614;