rs2378627

chr1-223058670-A-G

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 0.333 in 152,098 control chromosomes in the GnomAD database, including 8,677 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 0.33 (8677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50516 AN: 151980 Hom.: 8666 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.333 AC: 50577 AN: 152098 Hom.: 8677 Cov.: 32 AF XY: 0.332 AC XY: 24659 AN XY: 74336

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.312

Alfa AF: 0.352 Hom.: 1189

Bravo AF: 0.324

Asia WGS AF: 0.326 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.24
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378627; hg19: chr1-223232012;