rs1800790

Variant names:

• chr4-154562556-G-A
• rs1800790

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.155 in 151,852 control chromosomes in the GnomAD database, including 2,191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.15 (2191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 4-154562556-G-A is Benign according to our data. Variant chr4-154562556-G-A is described in ClinVar as [Benign]. Clinvar id is 16388.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 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: 0.155 AC: 23485 AN: 151734 Hom.: 2193 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.155 AC: 23489 AN: 151852 Hom.: 2191 Cov.: 32 AF XY: 0.153 AC XY: 11340 AN XY: 74226

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.173

Alfa AF: 0.185 Hom.: 470

Bravo AF: 0.151

Asia WGS AF: 0.158 AC: 548 AN: 3468

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

FIBRINOGEN-BETA POLYMORPHISM Benign:1

Jun 15, 1997

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800790; hg19: chr4-155483708;