rs1800790

Positions:

• chr4-154562556-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Benign, no assertion criteria provided

literature only

OMIM

Jun 15, 1997

- -

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;