rs1800791

Variant names:

• chr4-154562157-G-A
• rs1800791

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.154 in 151,944 control chromosomes in the GnomAD database, including 2,066 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 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: 0.154 AC: 23315 AN: 151826 Hom.: 2057 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.154 AC: 23329 AN: 151944 Hom.: 2066 Cov.: 32 AF XY: 0.157 AC XY: 11626 AN XY: 74248

African (AFR) AF: 0.123 AC: 5102 AN: 41472

American (AMR) AF: 0.265 AC: 4035 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3466

East Asian (EAS) AF: 0.0576 AC: 298 AN: 5172

South Asian (SAS) AF: 0.132 AC: 634 AN: 4812

European-Finnish (FIN) AF: 0.185 AC: 1957 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10343 AN: 67904

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.146 Hom.: 2211

Bravo AF: 0.156

Asia WGS AF: 0.119 AC: 412 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.9
DANN	Benign	0.43
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1800791; hg19: chr4-155483309;