chr1-24978623-T-C

Variant names:

• chr1-24978623-T-C
• rs6600247

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 0.548 in 151,990 control chromosomes in the GnomAD database, including 23,187 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 0.55 (23187 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83248 AN: 151872 Hom.: 23146 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.548 AC: 83326 AN: 151990 Hom.: 23187 Cov.: 31 AF XY: 0.558 AC XY: 41447 AN XY: 74294

African (AFR) AF: 0.556 AC: 23016 AN: 41426

American (AMR) AF: 0.664 AC: 10145 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3600 AN: 5172

South Asian (SAS) AF: 0.585 AC: 2825 AN: 4826

European-Finnish (FIN) AF: 0.560 AC: 5909 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34045 AN: 67962

Other (OTH) AF: 0.573 AC: 1211 AN: 2112

Alfa AF: 0.533 Hom.: 6318

Bravo AF: 0.561

Asia WGS AF: 0.665 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.46
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs6600247; hg19: chr1-25305114;