rs3756450

Positions:

• chr5-1448033-A-G
• chr5-1448033-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.231 in 152,110 control chromosomes in the GnomAD database, including 5,313 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.23 (5313 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 5-1448033-A-G is Benign according to our data. Variant chr5-1448033-A-G is described in ClinVar as [Benign]. Clinvar id is 2920605.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35192 AN: 151992 Hom.: 5321 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.231 AC: 35197 AN: 152110 Hom.: 5313 Cov.: 33 AF XY: 0.236 AC XY: 17563 AN XY: 74372

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.212

Alfa AF: 0.150 Hom.: 3199

Bravo AF: 0.245

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Schizophrenia Benign:1

Benign, criteria provided, single submitter

case-control

Center for Forensic Mental Health, Chiba University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.51
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756450; hg19: chr5-1448148;