chr5-1448033-A-G

Variant names:

• chr5-1448033-A-G
• rs3756450

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.386 AC: 16031 AN: 41494

American (AMR) AF: 0.269 AC: 4115 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3472

East Asian (EAS) AF: 0.448 AC: 2307 AN: 5150

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1719 AN: 10600

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8495 AN: 67976

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.170 Hom.: 6749

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

-

Center for Forensic Mental Health, Chiba University

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: case-control

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.51
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3756450; hg19: chr5-1448148;