rs2486674

Variant names:

• chr1-28093873-A-G
• rs2486674

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 0.207 in 142,360 control chromosomes in the GnomAD database, including 3,198 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 0.21 (3198 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 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: 0.207 AC: 29509 AN: 142264 Hom.: 3200 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.207 AC: 29527 AN: 142360 Hom.: 3198 Cov.: 31 AF XY: 0.209 AC XY: 14608 AN XY: 69912

African (AFR) AF: 0.117 AC: 4409 AN: 37562

American (AMR) AF: 0.178 AC: 2615 AN: 14664

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 745 AN: 3396

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5168

South Asian (SAS) AF: 0.197 AC: 930 AN: 4726

European-Finnish (FIN) AF: 0.275 AC: 2845 AN: 10354

Middle Eastern (MID) AF: 0.235 AC: 63 AN: 268

European-Non Finnish (NFE) AF: 0.252 AC: 15993 AN: 63384

Other (OTH) AF: 0.210 AC: 407 AN: 1938

Alfa AF: 0.224 Hom.: 7461

Bravo AF: 0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.4
DANN	Benign	0.90
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs2486674; hg19: chr1-28420384;