rs2363451

Variant names:

• chr1-199894427-A-G
• rs2363451

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.0875

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0775

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0904 Hom.: 386

Bravo AF: 0.155

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2363451; hg19: chr1-199863555;