1-4282544-G-A

Variant names:

• chr1-4282544-G-A
• rs1495244

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 0.374 in 151,960 control chromosomes in the GnomAD database, including 12,884 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 0.37 (12884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.374 AC: 56815 AN: 151842 Hom.: 12846 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.374 AC: 56908 AN: 151960 Hom.: 12884 Cov.: 32 AF XY: 0.375 AC XY: 27842 AN XY: 74274

African (AFR) AF: 0.644 AC: 26679 AN: 41426

American (AMR) AF: 0.260 AC: 3980 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3462

East Asian (EAS) AF: 0.396 AC: 2041 AN: 5156

South Asian (SAS) AF: 0.354 AC: 1700 AN: 4808

European-Finnish (FIN) AF: 0.321 AC: 3384 AN: 10544

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17282 AN: 67962

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.294 Hom.: 9749

Bravo AF: 0.383

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.32
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1495244; hg19: chr1-4342604;