chr1-24193430-G-A

Variant names:

• chr1-24193430-G-A
• rs4649203

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 0.615 in 151,962 control chromosomes in the GnomAD database, including 31,201 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 0.61 (31201 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 54 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 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: 0.615 AC: 93443 AN: 151844 Hom.: 31202 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.615 AC: 93437 AN: 151962 Hom.: 31201 Cov.: 31 AF XY: 0.620 AC XY: 46005 AN XY: 74256

African (AFR) AF: 0.331 AC: 13719 AN: 41410

American (AMR) AF: 0.769 AC: 11745 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2324 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3141 AN: 5136

South Asian (SAS) AF: 0.663 AC: 3187 AN: 4806

European-Finnish (FIN) AF: 0.701 AC: 7402 AN: 10566

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49688 AN: 67984

Other (OTH) AF: 0.635 AC: 1342 AN: 2112

Alfa AF: 0.697 Hom.: 131542

Bravo AF: 0.610

Asia WGS AF: 0.575 AC: 1999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4649203; hg19: chr1-24519920; COSMIC: COSV59931770;