rs1800790

Variant names:

• chr4-154562556-G-A
• rs1800790

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 296 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0513 AC: 2126 AN: 41482

American (AMR) AF: 0.144 AC: 2201 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3464

East Asian (EAS) AF: 0.217 AC: 1124 AN: 5174

South Asian (SAS) AF: 0.156 AC: 753 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1866 AN: 10562

Middle Eastern (MID) AF: 0.228 AC: 66 AN: 290

European-Non Finnish (NFE) AF: 0.208 AC: 14072 AN: 67784

Other (OTH) AF: 0.173 AC: 365 AN: 2110

Alfa AF: 0.141 Hom.: 540

Bravo AF: 0.151

Asia WGS AF: 0.158 AC: 548 AN: 3468

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	FIBRINOGEN-BETA POLYMORPHISM (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.42
PromoterAI		0.0012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1800790; hg19: chr4-155483708;