rs3813627

chr1-161225358-G-T

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 0.288 in 152,158 control chromosomes in the GnomAD database, including 7,246 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 0.29 (7246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.288 AC: 43794 AN: 152040 Hom.: 7246 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.288 AC: 43801 AN: 152158 Hom.: 7246 Cov.: 32 AF XY: 0.289 AC XY: 21516 AN XY: 74382

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.306

Alfa AF: 0.328 Hom.: 3121

Bravo AF: 0.285

Asia WGS AF: 0.435 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.5
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813627; hg19: chr1-161195148;