chr1-199894427-A-G

Variant names:

• chr1-199894427-A-G
• rs2363451

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 0.148 in 152,194 control chromosomes in the GnomAD database, including 2,552 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 0.15 (2552 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22433 AN: 152076 Hom.: 2554 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.148 AC: 22452 AN: 152194 Hom.: 2552 Cov.: 33 AF XY: 0.144 AC XY: 10745 AN XY: 74422

African (AFR) AF: 0.318 AC: 13197 AN: 41498

American (AMR) AF: 0.0875 AC: 1338 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5180

South Asian (SAS) AF: 0.0929 AC: 449 AN: 4834

European-Finnish (FIN) AF: 0.100 AC: 1061 AN: 10592

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0775 AC: 5268 AN: 68014

Other (OTH) AF: 0.125 AC: 263 AN: 2110

Alfa AF: 0.0926 Hom.: 466

Bravo AF: 0.155

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2363451; hg19: chr1-199863555;